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* 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).
* gnu: edirect: Update to 4.10.Ricardo Wurmus2016-05-04
| | | | * gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
* gnu: Add muscle.Ben Woodcroft2016-04-30
| | | | * gnu/packages/bioinformatics.scm (muscle): New variable.
* gnu: r-acsnminer: Update to 0.16.01.29.Ricardo Wurmus2016-04-26
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
* gnu: r-qtl: Update to 1.39-5.Ricardo Wurmus2016-04-26
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
* gnu: Add filevercmp.Roel Janssen2016-04-26
| | | | * gnu/packages/bioinformatics.scm (filevercmp): New variable.
* gnu: samtools: Update to 1.3.1.Ben Woodcroft2016-04-24
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
* gnu: Rename Java packages to match new naming specification.Hartmut Goebel2016-04-19
| | | | | | | | | | | | * 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".
* gnu: python2-plastid: Propagate setuptools.Ricardo Wurmus2016-04-19
| | | | | | * gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move python2-setuptools from here... [propagated-inputs]: ...to here.
* gnu: Add python-plastid.Ricardo Wurmus2016-04-19
| | | | | * gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New variables.
* gnu: Add python-twobitreader.Ricardo Wurmus2016-04-19
| | | | | * gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader): New variables.
* gnu: packages: Use 'search-patches' everywhere.Alex Kost2016-04-14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.Ricardo Wurmus2016-04-11
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): New variable.
* gnu: Add r-bsgenome-celegans-ucsc-ce6.Ricardo Wurmus2016-04-11
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New variable.
* gnu: Add r-bsgenome-mmusculus-ucsc-mm9.Ricardo Wurmus2016-04-11
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New variable.
* gnu: Add r-motifrg.Ricardo Wurmus2016-04-11
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): New variable.
* gnu: Add r-bsgenome-hsapiens-ucsc-hg19.Ricardo Wurmus2016-04-11
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New variable.
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