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2016-03-01gnu: r-go-db: Bioconductor changed URL for data downloads....* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL. Pjotr Prins
2016-03-01gnu: r-iranges: Update to 2.4.8....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8. Pjotr Prins
2016-03-01gnu: r-s4vectors: Update to 0.8.11....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11. Pjotr Prins
2016-03-01gnu: Add PePr....* gnu/packages/bioinformatics.scm (pepr): New variable. Ricardo Wurmus
2016-03-01gnu: Add bwa-pssm....* gnu/packages/bioinformatics.scm (bwa-pssm): New variable. Ricardo Wurmus
2016-02-27gnu: Fix misplaced commas (unquote)....Fix many occurrences of comma (unquote) being placed immediately after the previous list item, e.g. ("ncurses", ncurses) in the inputs. * gnu/packages/base.scm (patch, gnu-make), gnu/packages/bioinformatics.scm (hmmer), gnu/packages/bittorrent.scm (aria2), gnu/packages/compression.scm (pbzip2), gnu/packages/databases.scm (recutils), gnu/packages/fonts.scm (font-terminus), gnu/packages/freedesktop.scm (xdg-utils, elogind), gnu/packages/games.scm (gnujump), gnu/packages/gnome.scm (libidl, gnumeric, eog, gedit), gnu/packages/gnunet.scm (gnunet), gnu/packages/gnuzilla.scm (mozjs, nspr), gnu/packages/gtk.scm (gtksourceview, gdk-pixbuf), gnu/packages/lua.scm (lua), gnu/packages/openstack.scm (python-swiftclient), gnu/packages/perl.scm (perl-json-any), gnu/packages/polkit.scm (polkit-qt), gnu/packages/python.scm (wrap-python3, python-oauthlib) (python-mccabe-0.2.1, python-contextlib2, python2-rauth), gnu/packages/qt.scm (qtkeychain), gnu/packages/ruby.scm (ruby-nokogiri), gnu/packages/screen.scm (screen), gnu/packages/ssh.scm (libssh), gnu/packages/video.scm (ffmpeg, mplayer), gnu/packages/vim.scm (vim), gnu/packages/xdisorg.scm (redshift), gnu/packages/xfce.scm (xfce4-panel, xfce4-settings), gnu/packages/xnee.scm (xnee), gnu/packages/xorg.scm (font-adobe100dpi, font-adobe75dpi), gnu/packages/zsh.scm (zsh): Fix misplaced commas (unquote). Mark H Weaver
2016-02-25gnu: Add missing import in bioinformatics.scm....This is a followup to 1baee94. * gnu/packages/bioinformatics.scm: Add missing import. Ludovic Courtès
2016-02-25gnu: Add libBigWig....* gnu/packages/bioinformatics.scm (libbigwig): New variable. Ricardo Wurmus
2016-02-24gnu: r-topgo: Add missing input....* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add "r-graph". Ricardo Wurmus
2016-02-24gnu: Add r-graph....* gnu/packages/bioinformatics.scm (r-graph): New variable. Ricardo Wurmus
2016-02-24gnu: Add r-org-mm-eg-db....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable. Ricardo Wurmus
2016-02-24gnu: Add r-org-dm-eg-db....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable. Ricardo Wurmus
2016-02-24gnu: Add r-org-ce-eg-db....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable. Ricardo Wurmus
2016-02-24gnu: Add r-org-hs-eg-db....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable. Ricardo Wurmus
2016-02-16gnu: htseq: Add PySam to inputs....* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam". Ricardo Wurmus
2016-02-16gnu: Add StringTie....* gnu/packages/bioinformatics.scm (stringtie): New variable. Ricardo Wurmus
2016-02-16gnu: prodigal: Update to 2.6.3....* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3. Ben Woodcroft
2016-02-15gnu: r-annotationdbi: Update to 1.32.3....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3. Ricardo Wurmus
2016-02-15gnu: vsearch: Update to 1.10.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0. [origin]: Adapt to changes in bundling of cityhash. Ben Woodcroft
2016-02-12gnu: macs: Update to 2.1.0.20151222....* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222. Ricardo Wurmus
2016-02-12gnu: macs: Use "pypi-uri"....* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to build source URI. Ricardo Wurmus
2016-02-02gnu: Update sortmerna to 2.1....* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1. Ben J. Woodcroft
2016-01-26gnu: sra-tools: Update to 2.5.7....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7. Ben Woodcroft
2016-01-26gnu: ncbi-vdb: Update to 2.5.7....gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7. Ben Woodcroft
2016-01-26gnu: ngs-sdk: Update to 1.2.3....gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3. Ben Woodcroft
2016-01-25gnu: Add sortmerna....* gnu/packages/bioinformatics.scm (sortmerna): New variable. Ben Woodcroft
2016-01-23gnu: Add cufflinks....* gnu/packages/bioinformatics.scm (cufflinks): New variable. Ricardo Wurmus
2016-01-23gnu: Add TopHat....* gnu/packages/bioinformatics.scm (tophat): New variable. * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Ricardo Wurmus
2016-01-23gnu: star: Update to 2.5.1b....* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b. [source]: Remove bundled htslib sources and pre-built binaries. [arguments]: Add phase "do-not-use-bundled-htslib". [inputs]: Add "htslib". Ricardo Wurmus
2016-01-23gnu: star: Use "modify-phases" syntax....* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax. Ricardo Wurmus
2016-01-21gnu: r-qtl: Update to 1.38-4....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4. Pjotr Prins
2016-01-16gnu: samtools-0.1: Adapt to changes in "samtools" variable....* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add "LIBCURSES" make flag; delete "configure" phase; disable tests outside of "substitute-keyword-arguments". Ricardo Wurmus
2016-01-14gnu: r-go-db: Add missing input....* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi". Ricardo Wurmus
2016-01-14gnu: bowtie: Update to 2.2.6....* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6. [source]: Remove patch; do not set CC and CPP variables. [inputs]: Add "tbb". [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom "install" phase. * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch file. Ricardo Wurmus
2016-01-14gnu: orfm: Update to 0.5.3....* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas. Ben Woodcroft
2016-01-13gnu: samtools: Update to 1.3....* gnu/packages/bioinformatics.scm (samtools): Update to 1.3. [arguments]: Enable tests for all architectures; set ncurses in configure-flags instead of make-flags; simplify "patch-tests" phase; restore "configure" phase. Ricardo Wurmus
2016-01-12gnu: Add fxtract....* gnu/packages/bioinformatics.scm (fxtract): New variable. Ben Woodcroft
2016-01-11gnu: bedtools: Update to 2.25.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. Ben Woodcroft
2016-01-11gnu: bedtools: Use modify-phases....* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases. Ben Woodcroft
2016-01-08gnu: Add missing (gnu packages gcc) import....* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'. Mathieu Lirzin
2016-01-07gnu: Add genomation....* gnu/packages/bioinformatics.scm (r-genomation): New variable. Ricardo Wurmus
2016-01-07gnu: Add seqPattern....* gnu/packages/bioinformatics.scm (r-seqpattern): New variable. Ricardo Wurmus
2016-01-07gnu: Add impute....* gnu/packages/bioinformatics.scm (r-impute): New variable. Ricardo Wurmus
2016-01-07gnu: Add BSgenome....* gnu/packages/bioinformatics.scm (r-bsgenome): New variable. Ricardo Wurmus
2016-01-07gnu: Add topGO....* gnu/packages/bioinformatics.scm (r-topgo): New variable. Ricardo Wurmus
2016-01-07gnu: Add GO.db....* gnu/packages/bioinformatics.scm (r-go-db): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicFeatures....* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable. Ricardo Wurmus
2016-01-07gnu: Add rtracklayer....* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicAlignments....* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable. Ricardo Wurmus
2016-01-07gnu: Add SummarizedExperiment....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable. Ricardo Wurmus
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