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2016-03-10gnu: Add bioawk.Roel Janssen
* gnu/packages/bioinformatics.scm (bioawk): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-03gnu: python-pysam: Move cython and setuptools to native inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move "python-cython" and "python-setuptools" from here... [native-inputs]: ... to here.
2016-03-03gnu: deeptools: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1. [inputs]: Add "python2-numpydoc" and "python2-pybigwig".
2016-03-03gnu: deeptools: Change "propagated-inputs" to "inputs".Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move all inputs from here... [inputs]: ...to here.
2016-03-03gnu: Add python-pybigwig.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig): New variables.
2016-03-03gnu: python-pysam: Update to 0.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to... * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): ...here.
2016-03-01gnu: r-go-db: Bioconductor changed URL for data downloads.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01gnu: r-iranges: Update to 2.4.8.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01gnu: r-s4vectors: Update to 0.8.11.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01gnu: Add PePr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01gnu: Add bwa-pssm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-02-27gnu: Fix misplaced commas (unquote).Mark H Weaver
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).
2016-02-25gnu: Add missing import in bioinformatics.scm.Ludovic Courtès
This is a followup to 1baee94. * gnu/packages/bioinformatics.scm: Add missing import.
2016-02-25gnu: Add libBigWig.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
2016-02-24gnu: r-topgo: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add "r-graph".
2016-02-24gnu: Add r-graph.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): New variable.
2016-02-24gnu: Add r-org-mm-eg-db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
2016-02-24gnu: Add r-org-dm-eg-db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
2016-02-24gnu: Add r-org-ce-eg-db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
2016-02-24gnu: Add r-org-hs-eg-db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
2016-02-16gnu: htseq: Add PySam to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
2016-02-16gnu: Add StringTie.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stringtie): New variable.
2016-02-16gnu: prodigal: Update to 2.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
2016-02-15gnu: r-annotationdbi: Update to 1.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
2016-02-15gnu: vsearch: Update to 1.10.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0. [origin]: Adapt to changes in bundling of cityhash.
2016-02-12gnu: macs: Update to 2.1.0.20151222.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
2016-02-12gnu: macs: Use "pypi-uri".Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to build source URI.
2016-02-02gnu: Update sortmerna to 2.1.Ben J. Woodcroft
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
2016-01-26gnu: sra-tools: Update to 2.5.7.Ben Woodcroft
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
2016-01-26gnu: ncbi-vdb: Update to 2.5.7.Ben Woodcroft
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
2016-01-26gnu: ngs-sdk: Update to 1.2.3.Ben Woodcroft
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
2016-01-25gnu: Add sortmerna.Ben Woodcroft
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
2016-01-23gnu: Add cufflinks.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
2016-01-23gnu: Add TopHat.Ricardo Wurmus
* 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.
2016-01-23gnu: star: Update to 2.5.1b.Ricardo Wurmus
* 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".
2016-01-23gnu: star: Use "modify-phases" syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax.
2016-01-21gnu: r-qtl: Update to 1.38-4.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
2016-01-16gnu: samtools-0.1: Adapt to changes in "samtools" variable.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add "LIBCURSES" make flag; delete "configure" phase; disable tests outside of "substitute-keyword-arguments".
2016-01-14gnu: r-go-db: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
2016-01-14gnu: bowtie: Update to 2.2.6.Ricardo Wurmus
* 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.
2016-01-14gnu: orfm: Update to 0.5.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
2016-01-13gnu: samtools: Update to 1.3.Ricardo Wurmus
* 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.
2016-01-12gnu: Add fxtract.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-11gnu: bedtools: Update to 2.25.0.Ben Woodcroft
* 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.
2016-01-11gnu: bedtools: Use modify-phases.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-08gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
2016-01-07gnu: Add genomation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
2016-01-07gnu: Add seqPattern.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
2016-01-07gnu: Add impute.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): New variable.
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