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* Merge branch 'master' into core-updatesLudovic Courtès2016-06-27
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* gnu: Add r-bsgenome-mmusculus-ucsc-mm10.Ricardo Wurmus2016-06-15
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New variable.
* gnu: Add ruby-bio-kseq.Ben Woodcroft2016-06-14
| | | | * gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
* gnu: piranha: Update to 1.2.1.Ricardo Wurmus2016-06-13
| | | | * gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
* gnu: Use full SHA1 commit ids.Hartmut Goebel2016-06-05
| | | | | | | | | | | | | | | * 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>
* gnu: diamond: Update to 0.8.5.Ben Woodcroft2016-06-04
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
* gnu: Add r-genomationdata.Ricardo Wurmus2016-05-31
| | | | * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
* gnu: Update diamond to 0.8.3.Ben Woodcroft2016-05-28
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
* gnu: Add ParDRe.Ricardo Wurmus2016-05-23
| | | | * gnu/packages/bioinformatics.scm (pardre): New variable.
* gnu: r-genomation: Update to 1.4.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
* gnu: r-genomicfeatures: Update to 1.24.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
* gnu: r-summarizedexperiment: Update to 1.2.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
* gnu: r-biocparallel: Update to 1.6.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
* gnu: r-annotationdbi: Update to 1.34.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
* gnu: r-variantannotation: Update to 1.18.1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
* gnu: r-genomeinfodb: Update to 1.8.1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
* gnu: diamond: Do not specify target architecture.Ben Woodcroft2016-05-18
| | | | | * gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture.
* gnu: Add Piranha.Ricardo Wurmus2016-05-18
| | | | * gnu/packages/bioinformatics.scm (piranha): New variable.
* gnu: sortmerna: Update to 2.1b.Ben Woodcroft2016-05-17
| | | | | * gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b. [inputs]: New field.
* gnu: vsearch: Update to 1.11.1.Ben Woodcroft2016-05-17
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
* gnu: diamond: Update to 0.8.1.Ben Woodcroft2016-05-17
| | | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1. [source]: Remove 'snippet'. [build-system]: Use cmake-build-system. [arguments]: Remove modifications to phases. [native-inputs]: Remove field. [inputs]: Remove 'boost'.
* gnu: r-zlibbioc: Update to 1.18.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
* gnu: r-motifrg: Update to 1.16.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
* gnu: r-seqlogo: Update to 1.38.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
* gnu: r-genomation: Update to 1.4.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
* gnu: r-seqpattern: Update to 1.4.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
* gnu: r-impute: Update to 1.46.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
* gnu: r-bsgenome: Update to 1.40.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
* gnu: r-topgo: Update to 2.24.0.Ricardo Wurmus2016-05-16
| | | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0. [propagated-inputs]: Add r-matrixstats.
* gnu: r-graph: Update to 1.50.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
* gnu: r-genomicfeatures: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
* gnu: r-rtracklayer: Update to 1.32.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
* gnu: r-genomicalignments: Update to 1.8.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
* gnu: r-summarizedexperiment: Update to 1.2.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
* gnu: r-rsamtools: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
* gnu: r-biostrings: Update to 2.40.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
* gnu: r-biocparallel: Update to 1.6.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
* gnu: r-biomart: Update to 2.28.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
* gnu: r-annotationdbi: Update to 1.34.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
* gnu: r-biobase: Update to 2.32.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
* gnu: r-genomicranges: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
* gnu: r-xvector: Update to 0.12.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
* gnu: r-variantannotation: Update to 1.18.0.Ricardo Wurmus2016-05-16
| | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.0.
* gnu: r-genomeinfodb: Update to 1.8.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
* gnu: r-iranges: Update to 2.6.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
* gnu: r-s4vectors: Update to 0.10.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
* gnu: r-dnacopy: Update to 1.46.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
* gnu: r-biocgenerics: Update to 0.18.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
* gnu: hmmer: Update urls.Efraim Flashner2016-05-16
| | | | | | * gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to eddylab, with their downloads. [home-page]: Update to new homepage.
* gnu: Update module imports for asciidoc and doxygen.Mark H Weaver2016-05-12
| | | | | | | | | | | | | | | | This is a followup to commit 0573a923def01e54bf104e0015ade44ab42f694f. * gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm, gnu/packages/fcitx.scm, gnu/packages/fish.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm, gnu/packages/kodi.scm, gnu/packages/libreoffice.scm, gnu/packages/linux.scm, gnu/packages/messaging.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm, gnu/packages/serialization.scm, gnu/packages/version-control.scm, gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm, gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or (gnu packages doxygen) to (gnu packages documentation).
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