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2016-05-12gnu: Update module imports for asciidoc and doxygen.Mark H Weaver
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).
2016-05-04gnu: edirect: Update to 4.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
2016-04-30gnu: Add muscle.Ben Woodcroft
* gnu/packages/bioinformatics.scm (muscle): New variable.
2016-04-26gnu: r-acsnminer: Update to 0.16.01.29.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
2016-04-26gnu: r-qtl: Update to 1.39-5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
2016-04-26gnu: Add filevercmp.Roel Janssen
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
2016-04-24gnu: samtools: Update to 1.3.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
2016-04-19gnu: Rename Java packages to match new naming specification.Hartmut Goebel
* gnu/packages/bioinformatics.scm (htsjdk): Rename to... (java-htsjdk): ...this. (ngs-java): Rename to... (java-ngs): ...this. (ncbi-vdb)[arguments,inputs]: Use new name. * gnu/packages/java.scm (swt): Rename to... (java-swt): ...this. * gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use new name of package "swt".
2016-04-19gnu: python2-plastid: Propagate setuptools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move python2-setuptools from here... [propagated-inputs]: ...to here.
2016-04-19gnu: Add python-plastid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New variables.
2016-04-19gnu: Add python-twobitreader.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader): New variables.
2016-04-14gnu: packages: Use 'search-patches' everywhere.Alex Kost
* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field. * gnu/packages/acl.scm: Likewise. * gnu/packages/admin.scm: Likewise. * gnu/packages/algebra.scm: Likewise. * gnu/packages/animation.scm: Likewise. * gnu/packages/apr.scm: Likewise. * gnu/packages/audacity.scm: Likewise. * gnu/packages/audio.scm: Likewise. * gnu/packages/autotools.scm: Likewise. * gnu/packages/avahi.scm: Likewise. * gnu/packages/backup.scm: Likewise. * gnu/packages/base.scm: Likewise. * gnu/packages/bash.scm: Likewise. * gnu/packages/bioinformatics.scm: Likewise. * gnu/packages/cdrom.scm: Likewise. * gnu/packages/ci.scm: Likewise. * gnu/packages/cmake.scm: Likewise. * gnu/packages/cpio.scm: Likewise. * gnu/packages/cross-base.scm: Likewise. * gnu/packages/dico.scm: Likewise. * gnu/packages/doxygen.scm: Likewise. * gnu/packages/ebook.scm: Likewise. * gnu/packages/elf.scm: Likewise. * gnu/packages/emacs.scm: Likewise. * gnu/packages/engineering.scm: Likewise. * gnu/packages/firmware.scm: Likewise. * gnu/packages/flashing-tools.scm: Likewise. * gnu/packages/fltk.scm: Likewise. * gnu/packages/ftp.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gawk.scm: Likewise. * gnu/packages/gcc.scm: Likewise. * gnu/packages/gd.scm: Likewise. * gnu/packages/ghostscript.scm: Likewise. * gnu/packages/glib.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/gnucash.scm: Likewise. * gnu/packages/gnunet.scm: Likewise. * gnu/packages/gnupg.scm: Likewise. * gnu/packages/gnuzilla.scm: Likewise. * gnu/packages/graphics.scm: Likewise. * gnu/packages/grub.scm: Likewise. * gnu/packages/gtk.scm: Likewise. * gnu/packages/guile.scm: Likewise. * gnu/packages/icu4c.scm: Likewise. * gnu/packages/idutils.scm: Likewise. * gnu/packages/image.scm: Likewise. * gnu/packages/imagemagick.scm: Likewise. * gnu/packages/irc.scm: Likewise. * gnu/packages/ldc.scm: Likewise. * gnu/packages/libcanberra.scm: Likewise. * gnu/packages/libevent.scm: Likewise. * gnu/packages/libreoffice.scm: Likewise. * gnu/packages/libunwind.scm: Likewise. * gnu/packages/libusb.scm: Likewise. * gnu/packages/linux.scm: Likewise. * gnu/packages/lirc.scm: Likewise. * gnu/packages/llvm.scm: Likewise. * gnu/packages/lsh.scm: Likewise. * gnu/packages/lua.scm: Likewise. * gnu/packages/lxqt.scm: Likewise. * gnu/packages/mail.scm: Likewise. * gnu/packages/maths.scm: Likewise. * gnu/packages/mcrypt.scm: Likewise. * gnu/packages/messaging.scm: Likewise. * gnu/packages/mit-krb5.scm: Likewise. * gnu/packages/mp3.scm: Likewise. * gnu/packages/multiprecision.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/ninja.scm: Likewise. * gnu/packages/nvi.scm: Likewise. * gnu/packages/ocaml.scm: Likewise. * gnu/packages/orpheus.scm: Likewise. * gnu/packages/ots.scm: Likewise. * gnu/packages/parallel.scm: Likewise. * gnu/packages/patchutils.scm: Likewise. * gnu/packages/pcre.scm: Likewise. * gnu/packages/pdf.scm: Likewise. * gnu/packages/perl.scm: Likewise. * gnu/packages/plotutils.scm: Likewise. * gnu/packages/polkit.scm: Likewise. * gnu/packages/pulseaudio.scm: Likewise. * gnu/packages/python.scm: Likewise. * gnu/packages/qemu.scm: Likewise. * gnu/packages/qt.scm: Likewise. * gnu/packages/ratpoison.scm: Likewise. * gnu/packages/rdf.scm: Likewise. * gnu/packages/readline.scm: Likewise. * gnu/packages/rush.scm: Likewise. * gnu/packages/scheme.scm: Likewise. * gnu/packages/screen.scm: Likewise. * gnu/packages/sdl.scm: Likewise. * gnu/packages/slim.scm: Likewise. * gnu/packages/ssh.scm: Likewise. * gnu/packages/tcl.scm: Likewise. * gnu/packages/tcsh.scm: Likewise. * gnu/packages/texinfo.scm: Likewise. * gnu/packages/tls.scm: Likewise. * gnu/packages/tor.scm: Likewise. * gnu/packages/tv.scm: Likewise. * gnu/packages/valgrind.scm: Likewise. * gnu/packages/version-control.scm: Likewise. * gnu/packages/video.scm: Likewise. * gnu/packages/vpn.scm: Likewise. * gnu/packages/vtk.scm: Likewise. * gnu/packages/w3m.scm: Likewise. * gnu/packages/web.scm: Likewise. * gnu/packages/wicd.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/xdisorg.scm: Likewise. * gnu/packages/xfce.scm: Likewise. * gnu/packages/xiph.scm: Likewise. * gnu/packages/xml.scm: Likewise. * gnu/packages/xorg.scm: Likewise. * gnu/packages/zip.scm: Likewise.
2016-04-11gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): New variable.
2016-04-11gnu: Add r-bsgenome-celegans-ucsc-ce6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New variable.
2016-04-11gnu: Add r-bsgenome-mmusculus-ucsc-mm9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New variable.
2016-04-11gnu: Add r-motifrg.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
2016-04-11gnu: Add r-bsgenome-hsapiens-ucsc-hg19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New variable.
2016-04-11gnu: Add r-seqlogo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
2016-04-06gnu: Add r-zlibbioc.Roel Janssen
* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06gnu: Add r-variantannotation.Roel Janssen
* gnu/packages/bioinformatics.scm (r-variantannotation): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-05gnu: vcftools: Update to 0.1.14.Roel Janssen
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14. [arguments]: Do not modify phases as it is not needed anymore. [native-inputs]: Add 'pkg-config'. [home-page]: Update to new location. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-03-30gnu: python2-pbcore: Update to 1.2.8.Efraim Flashner
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8. [native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
2016-03-30gnu: r-genomation: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
2016-03-30gnu: r-genomicfeatures: Update to 1.22.13.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.22.13.
2016-03-30gnu: r-rtracklayer: Update to 1.30.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
2016-03-30gnu: r-genomicalignments: Update to 1.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.6.3.
2016-03-30gnu: r-summarizedexperiment: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.0.2.
2016-03-30gnu: r-biostrings: Update to 2.38.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
2016-03-30gnu: r-genomicranges: Update to 1.22.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
2016-03-30gnu: r-genomeinfodb: Update to 1.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
2016-03-24gnu: Remove "r-repository" property.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]: Remove "r-repository" property.
2016-03-18gnu: r-dnacopy: Fix home page URL.Ludovic Courtès
* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing URI scheme.
2016-03-17gnu: bless: Remove bundled sources for sparsehash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bless)[source]: Delete "google-sparsehash" sources. [inputs]: Add "sparsehash".
2016-03-17gnu: Add CD-HIT.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
2016-03-16gnu: Add r-dnacopy.Roel Janssen
* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
2016-03-16gnu: Add codingquarry.Rob Syme
* gnu/packages/bioinformatics.scm (codingquarry): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-14gnu: htsjdk: Use ant-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use ant-build-system. [arguments]: Adapt for ant-build-system.
2016-03-14gnu: Add pyicoteo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
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.
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