| Age | Commit message (Expand) | Author |
|---|
| 2016-05-04 | gnu: edirect: Update to 4.10....* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
| Ricardo Wurmus |
| 2016-04-30 | gnu: Add muscle....* gnu/packages/bioinformatics.scm (muscle): New variable.
| Ben Woodcroft |
| 2016-04-26 | gnu: r-acsnminer: Update to 0.16.01.29....* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
| Ricardo Wurmus |
| 2016-04-26 | gnu: r-qtl: Update to 1.39-5....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
| Ricardo Wurmus |
| 2016-04-26 | gnu: Add filevercmp....* gnu/packages/bioinformatics.scm (filevercmp): New variable.
| Roel Janssen |
| 2016-04-24 | gnu: samtools: Update to 1.3.1....* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
| Ben Woodcroft |
| 2016-04-19 | gnu: Rename Java packages to match new naming specification....* 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".
| Hartmut Goebel |
| 2016-04-19 | gnu: python2-plastid: Propagate setuptools....* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2016-04-19 | gnu: Add python-plastid....* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
variables.
| Ricardo Wurmus |
| 2016-04-19 | gnu: Add python-twobitreader....* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader): New variables.
| Ricardo Wurmus |
| 2016-04-14 | gnu: packages: Use 'search-patches' everywhere....* 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.
| Alex Kost |
| 2016-04-11 | gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3....* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
New variable.
| Ricardo Wurmus |
| 2016-04-11 | gnu: Add r-bsgenome-celegans-ucsc-ce6....* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
variable.
| Ricardo Wurmus |
| 2016-04-11 | gnu: Add r-bsgenome-mmusculus-ucsc-mm9....* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
variable.
| Ricardo Wurmus |
| 2016-04-11 | gnu: Add r-motifrg....* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
| Ricardo Wurmus |
| 2016-04-11 | gnu: Add r-bsgenome-hsapiens-ucsc-hg19....* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
variable.
| Ricardo Wurmus |
| 2016-04-11 | gnu: Add r-seqlogo....* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
| Ricardo Wurmus |
| 2016-04-06 | gnu: Add r-zlibbioc....* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Roel Janssen |
| 2016-04-06 | gnu: Add r-variantannotation....* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Roel Janssen |
| 2016-04-05 | gnu: vcftools: Update to 0.1.14....* 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>
| Roel Janssen |
| 2016-03-30 | gnu: python2-pbcore: Update to 1.2.8....* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8.
[native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
| Efraim Flashner |
| 2016-03-30 | gnu: r-genomation: Update to 1.2.2....* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-genomicfeatures: Update to 1.22.13....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to
1.22.13.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-rtracklayer: Update to 1.30.4....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-genomicalignments: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.6.3.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-summarizedexperiment: Update to 1.0.2....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.0.2.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-biostrings: Update to 2.38.4....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-genomicranges: Update to 1.22.4....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
| Ricardo Wurmus |
| 2016-03-30 | gnu: r-genomeinfodb: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
| Ricardo Wurmus |
| 2016-03-24 | gnu: Remove "r-repository" property....* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors,
r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]:
Remove "r-repository" property.
| Ricardo Wurmus |
| 2016-03-18 | gnu: r-dnacopy: Fix home page URL....* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing
URI scheme.
| Ludovic Courtès |
| 2016-03-17 | gnu: bless: Remove bundled sources for sparsehash....* gnu/packages/bioinformatics.scm (bless)[source]: Delete
"google-sparsehash" sources.
[inputs]: Add "sparsehash".
| Ricardo Wurmus |
| 2016-03-17 | gnu: Add CD-HIT....* gnu/packages/bioinformatics.scm (cd-hit): New variable.
| Ricardo Wurmus |
| 2016-03-16 | gnu: Add r-dnacopy....* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
| Roel Janssen |
| 2016-03-16 | gnu: Add codingquarry....* gnu/packages/bioinformatics.scm (codingquarry): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Rob Syme |
| 2016-03-14 | gnu: htsjdk: Use ant-build-system....* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.
| Ricardo Wurmus |
| 2016-03-14 | gnu: Add pyicoteo....* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
| Ricardo Wurmus |
| 2016-03-10 | gnu: Add bioawk....* gnu/packages/bioinformatics.scm (bioawk): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Roel Janssen |
| 2016-03-03 | gnu: python-pysam: Move cython and setuptools to native inputs....* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
| Ricardo Wurmus |
| 2016-03-03 | gnu: deeptools: Update to 2.1.1....* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
| Ricardo Wurmus |
| 2016-03-03 | gnu: deeptools: Change "propagated-inputs" to "inputs"....* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
| Ricardo Wurmus |
| 2016-03-03 | gnu: Add python-pybigwig....* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
New variables.
| Ricardo Wurmus |
| 2016-03-03 | gnu: python-pysam: Update to 0.8.4....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
| Ricardo Wurmus |
| 2016-03-03 | gnu: python-pysam, python2-pysam: Move to bioinformatics.scm....* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
...here.
| Ricardo Wurmus |
| 2016-03-01 | gnu: r-go-db: Bioconductor changed URL for data downloads....* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
| Pjotr Prins |
| 2016-03-01 | gnu: r-iranges: Update to 2.4.8....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
| Pjotr Prins |
| 2016-03-01 | gnu: r-s4vectors: Update to 0.8.11....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
| Pjotr Prins |
| 2016-03-01 | gnu: Add PePr....* gnu/packages/bioinformatics.scm (pepr): New variable.
| Ricardo Wurmus |
| 2016-03-01 | gnu: Add bwa-pssm....* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
| Ricardo Wurmus |
| 2016-02-27 | gnu: 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 |
