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* gnu: diamond: Update to 0.8.16.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16. Ben Woodcroft2016-07-27
* gnu: fasttree: Update to 2.1.9.•••* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9. Ben Woodcroft2016-07-23
* gnu: Update URLs for sourceforge.net.•••* 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. Leo Famulari2016-07-21
* gnu: diamond: Update to 0.8.15.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15. Ben Woodcroft2016-07-18
* gnu: eigensoft: Do not refer to "lapacke" output.•••* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference to non-existing "lapacke" output. Ricardo Wurmus2016-07-17
* gnu: Add eigensoft.•••* gnu/packages/bioinformatics.scm (eigensoft): New variable. Ricardo Wurmus2016-07-14
* gnu: Add Ribotaper.•••* gnu/packages/bioinformatics.scm (ribotaper): New variable. Ricardo Wurmus2016-07-12
* gnu: Add bedtools-2.18.•••* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable. Ricardo Wurmus2016-07-12
* gnu: diamond: Update to 0.8.12.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12. Ben Woodcroft2016-07-10
* gnu: Add python-dendropy.•••* 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. Ben Woodcroft2016-07-09
* gnu: star: Restrict supported systems to 64-bit systems.•••* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to x86_64-linux and mips64el-linux. Ben Woodcroft2016-07-08
* gnu: bedtools: Update to 2.26.0.•••* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0. Ben Woodcroft2016-07-07
* gnu: diamond: Update to 0.8.11.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11. Ben Woodcroft2016-07-07
* gnu: Add r-seqinr.•••* gnu/packages/bioinformatics.scm (r-seqinr): New variable. Ricardo Wurmus2016-07-07
* gnu: khmer: Limit to x86_64 systems only.•••* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field. Efraim Flashner2016-07-07
* gnu: Add multiqc.•••* gnu/packages/bioinformatics.scm (multiqc): New variable. Ricardo Wurmus2016-07-05
* gnu: Add bits.•••* gnu/packages/bioinformatics.scm (bits): New variable. Ricardo Wurmus2016-07-05
* gnu: Add EMBOSS.•••* gnu/packages/bioinformatics.scm (emboss): New variable. Ricardo Wurmus2016-07-05
* gnu: Add r-edger.•••* gnu/packages/bioinformatics.scm (r-edger): New variable. Roel Janssen2016-07-04
* gnu: Add r-limma.•••* gnu/packages/bioinformatics.scm (r-limma): New variable. Roel Janssen2016-07-04
* gnu: vsearch: Update to 2.0.1.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1. Ben Woodcroft2016-07-01
* gnu: blast+: Update to 2.4.0.•••* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0. Ben Woodcroft2016-06-29
* gnu: star: Update to 2.5.2a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a. Ben Woodcroft2016-06-29
* gnu: htslib: Update to 1.3.1.•••* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1. Ben Woodcroft2016-06-29
* gnu: Add SEEK.•••* gnu/packages/bioinformatics.scm (seek): New variable. Ricardo Wurmus2016-06-28
* gnu: mafft: Update to 7.299.•••* gnu/packages/bioinformatics.scm (mafft): Update to 7.299. Ben Woodcroft2016-06-28
* gnu: metabat: Update to 0.26.3.•••* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3. [arguments]: Update include and linking paths accordingly. Ben Woodcroft2016-06-28
* gnu: diamond: Update to 0.8.9.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9. Ben Woodcroft2016-06-28
* gnu: Add khmer.•••* gnu/packages/bioinformatics.scm (khmer): New variable. * gnu/packages/patches/khmer-use-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Ben Woodcroft2016-06-27
* gnu: Add python-screed.•••* gnu/packages/bioinformatics.scm (python-screed, python2-screed): New variables. Ben Woodcroft2016-06-27
* gnu: vsearch: Update to 2.0.0.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0. Ben Woodcroft2016-06-26
* gnu: vsearch: Update to 0.11.2.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2. Ben Woodcroft2016-06-22
* gnu: Add r-vegan.•••* gnu/packages/bioinformatics.scm (r-vegan): New variable. Ben Woodcroft2016-06-21
* gnu: diamond: Update to 0.8.7.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7. Ben Woodcroft2016-06-21
* gnu: Add r-bsgenome-mmusculus-ucsc-mm10.•••* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New variable. Ricardo Wurmus2016-06-15
* gnu: Add ruby-bio-kseq.•••* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable. Ben Woodcroft2016-06-14
* gnu: piranha: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1. Ricardo Wurmus2016-06-13
* gnu: Use full SHA1 commit ids.•••* 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> Hartmut Goebel2016-06-05
* gnu: diamond: Update to 0.8.5.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5. Ben Woodcroft2016-06-04
* gnu: Add r-genomationdata.•••* gnu/packages/bioinformatics.scm (r-genomationdata): New variable. Ricardo Wurmus2016-05-31
* gnu: Update diamond to 0.8.3.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3. Ben Woodcroft2016-05-28
* gnu: Add ParDRe.•••* gnu/packages/bioinformatics.scm (pardre): New variable. Ricardo Wurmus2016-05-23
* gnu: r-genomation: Update to 1.4.2.•••* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2. Ricardo Wurmus2016-05-20
* gnu: r-genomicfeatures: Update to 1.24.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2. Ricardo Wurmus2016-05-20
* gnu: r-summarizedexperiment: Update to 1.2.2.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2. Ricardo Wurmus2016-05-20
* gnu: r-biocparallel: Update to 1.6.2.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2. Ricardo Wurmus2016-05-20
* gnu: r-annotationdbi: Update to 1.34.2.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2. Ricardo Wurmus2016-05-20
* gnu: r-variantannotation: Update to 1.18.1.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1. Ricardo Wurmus2016-05-20
* gnu: r-genomeinfodb: Update to 1.8.1.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1. Ricardo Wurmus2016-05-20
* gnu: diamond: Do not specify target architecture.•••* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture. Ben Woodcroft2016-05-18
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