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2017-10-18gnu: f-seq: Fix location of commons-cli.jar.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of commons-cli.jar in the wrapper script.
2017-10-14gnu: python-biopython: Update to 1.70.Cyril Roelandt
* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.
2017-10-13gnu: Add plink-ng.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng): New variable.
2017-10-13gnu: Add paml.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (paml): New variable.
2017-10-12gnu: clustal-omega: Update to 1.2.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.
2017-10-12gnu: f-seq: Truncate version string.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of the version string.
2017-10-11gnu: rcas-web: Update to 0.0.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
2017-10-07Merge branch 'master' into stagingMarius Bakke
2017-10-07gnu: vsearch: Update to 2.5.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
2017-09-24Merge branch 'master' into stagingMarius Bakke
2017-09-23gnu: proteinortho: Update to 5.16b.Ben Woodcroft
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
2017-09-22gnu: Use xxd instead of vim.Ricardo Wurmus
* gnu/packages/audio.scm (faust-2)[native-inputs]: Replace vim with xxd. * gnu/packages/avr.scm (microscheme)[native-inputs]: Likewise. * gnu/packages/bioinformatics.scm (star)[native-inputs]: Likewise. * gnu/packages/disk.scm (dosfstools)[native-inputs]: Likewise. * gnu/packages/package-management.scm (diffoscope)[inputs]: Likewise.
2017-09-20gnu: Use 'modify-phases' syntax.Kei Kebreau
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal, wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use 'modify-phases' syntax. * gnu/packages/algebra.scm (arb)[arguments]: Likewise. * gnu/packages/apr.scm (apr-util)[arguments]: Likewise. * gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano, lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound, zita-convolver, zita-alsa-pcmi)[arguments]: Likewise. * gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express, flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise. * gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise. * gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise. * gnu/packages/compression.scm (sharutils)[arguments]: Likewise. * gnu/packages/conky.scm (conky)[arguments]: Likewise. * gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise. * gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise. * gnu/packages/display-managers.scm (slim)[arguments]: Likewise. * gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise. * gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise. * gnu/packages/engineering.scm (pcb)[arguments]: Likewise. * gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise. * gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise. * gnu/packages/fltk.scm (fltk)[arguments]: Likewise. * gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise. * gnu/packages/gd.scm (perl-gd)[arguments]: Likewise. * gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise. * gnu/packages/glib.scm (glibmm)[arguments]: Likewise. * gnu/packages/gl.scm (glew)[arguments]: Likewise. * gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs, libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise. * gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise. * gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise. * gnu/packages/graphics.scm (agg)[arguments]: Likewise. * gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present, python2-pycairo)[arguments]: Likewise. * gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise. * gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise. * gnu/packages/hugs.scm (hugs)[arguments]: Likewise. * gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal) [arguments]: Likewise. * gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise. * gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise. * gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static, lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools) [arguments]: Likewise. * gnu/packages/lisp.scm (ccl)[arguments]: Likewise. * gnu/packages/lout.scm (lout)[arguments]: Likewise. * gnu/packages/lua.scm (luajit)[arguments]: Likewise. * gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise. * gnu/packages/mail.scm (exim)[arguments]: Likewise. * gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise. * gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun) [arguments]: Likewise. * gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise. * gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise. * gnu/packages/music.scm (solfege)[arguments]: Likewise. * gnu/packages/noweb.scm (noweb)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]: Likewise. * gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu, zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise. * gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]: Likewise. * gnu/packages/photo.scm (gphoto2)[arguments]: Likewise. * gnu/packages/popt.scm (popt)[arguments]: Likewise. * gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]: Likewise. * gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise. * gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy, python-sqlalchemy, python-docopt)[arguments]: Likewise. * gnu/packages/rdf.scm (lrdf)[arguments]: Likewise. * gnu/packages/regex.scm (tre)[arguments]: Likewise. * gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise. * gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise. * gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise. * gnu/packages/scheme.scm (racket)[arguments]: Likewise. * gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise. * gnu/packages/serveez.scm (serveez)[arguments]: Likewise. * gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise. * gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise. * gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise. * gnu/packages/tcl.scm (expect)[arguments]: Likewise. * gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise. * gnu/packages/textutils.scm (recode, libgtextutils)[arguments]: Likewise. * gnu/packages/time.scm (time)[arguments]: Likewise. * gnu/packages/tor.scm (privoxy)[arguments]: Likewise. * gnu/packages/uucp.scm (uucp)[arguments]: Likewise. * gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise. * gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise. * gnu/packages/web.scm (tinyproxy)[arguments]: Likewise. * gnu/packages/wicd.scm (wicd)[arguments]: Likewise. * gnu/packages/wm.scm (bspwm)[arguments]: Likewise. * gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise. * gnu/packages/xfce.scm (xfconf)[arguments]: Likewise. * gnu/packages/xfig.scm (transfig)[arguments]: Likewise. * gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-09-18gnu: r-rcas: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
2017-09-18gnu: r-rcas: Update to 1.3.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
2017-09-10gnu: Fix build failures caused by commitKei Kebreau
d10092b849153dc27cfed0a9601fde6c7bdec918. * gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase order. * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
2017-09-05gnu: Add r-sparql.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
2017-09-04gnu: Put autoconf-related phases immediately after the 'unpack phase.Kei Kebreau
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases accordingly. * gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss, htslib-for-sambamba)[arguments]: Likewise. * gnu/packages/ci.scm (cuirass)[arguments]: Likewise. * gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise. * gnu/packages/cpp.scm (libzen)[arguments]: Likewise. * gnu/packages/crypto.scm (opendht)[arguments]: Likewise. * gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise. * gnu/packages/debug.scm (stress-make)[arguments]: Likewise. * gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]: Likewise. * gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise. * gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise. * gnu/packages/engineering.scm (gerbv)[arguments]: Likewise. * gnu/packages/erlang.scm (erlang)[arguments]: Likewise. * gnu/packages/ftp.scm (weex)[arguments]: Likewise. * gnu/packages/gnome.scm (dia)[arguments]: Likewise. * gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise. * gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise. * gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]: Likewise. * gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise. * gnu/packages/irc.scm (weechat)[arguments]: Likewise. * gnu/packages/java.scm (classpath-devel)[arguments]: Likewise. * gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise. * gnu/packages/libusb.scm (hidapi)[arguments]: Likewise. * gnu/packages/linux.scm (gpm)[arguments]: Likewise. * gnu/packages/logging.scm (glog)[arguments]: Likewise. * gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise. * gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp) [arguments]: Likewise. * gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]: Likewise. * gnu/packages/microcom.scm (microcom)[arguments]: Likewise. * gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise. * gnu/packages/parallel.scm (slurm)[arguments]: Likewise. * gnu/packages/pdf.scm (libharu)[arguments]: Likewise. * gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise. * gnu/packages/serialization.scm (msgpack)[arguments]: Likewise. * gnu/packages/shells.scm (scsh)[arguments]: Likewise. * gnu/packages/telephony.scm (libiax2)[arguments]: Likewise. * gnu/packages/textutils.scm (dotconf)[arguments]: Likewise. * gnu/packages/version-control.scm (findnewest)[arguments]: Likewise. * gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
2017-09-01gnu: r-genomicalignments: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
2017-09-01gnu: r-vegan: Update to 2.4-4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4. [native-inputs]: Remove r-knitr.
2017-09-01gnu: r-maldiquant: Update to 1.16.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
2017-09-01gnu: r-bookdown: Update to 0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
2017-09-01gnu: r-rcas: Correct license.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01gnu: r-rcas: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
2017-09-01gnu: vsearch: Update to 2.4.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
2017-09-01gnu: metabat: Update to 2.12.1.Ben Woodcroft
* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1. [source]: Remove it. Use url-fetch.
2017-08-31gnu: bioinformatics: Work around more "dotless @INC" build failures.Ben Woodcroft
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add 'set-perl-search-path' phase.
2017-08-31gnu: metabat: Update to 2.11.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3. [source]: Use git-fetch. Remove boost-related patch. * gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-08-30gnu: multiqc: Update to 1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2. [source]: Remove patches. [arguments]: Remove to enable tests. [propagated-inputs]: Add python-spectra, python-requests, python-markdown, python-lzstring. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-08-21Merge branch 'master' into core-updatesMarius Bakke
2017-08-20gnu: Add r-annotationfilter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-08-17gnu: Add r-methylkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
2017-08-17gnu: Add r-qvalue.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
2017-08-17gnu: Add r-fastseg.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
2017-08-17gnu: Add r-annotationhub.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
2017-08-17gnu: Add r-interactivedisplaybase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
2017-08-16gnu: r-mzr: Fix building on aarch64 and armhf.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
2017-08-15gnu: diamond: Update to 0.9.10.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
2017-08-15gnu: bcftools: Fix building on aarch64.Efraim Flashner
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file. * gnu/packages/bioinformatics.scm (bcftools)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Register it.
2017-08-15Merge branch 'master' into core-updatesMark H Weaver
2017-08-14gnu: Add bismark.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark): New variable.
2017-08-14gnu: Add r-dexseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
2017-08-09Merge branch 'master' into core-updatesMark H Weaver
2017-08-09gnu: r-wgcna: Update to 1.61.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival.
2017-08-09gnu: Add reference to (gnu packages graph).Ricardo Wurmus
This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
2017-08-07Merge branch 'master' into core-updatesMark H Weaver
2017-08-07gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Restore hash from before the tarball changed in place. It changed back. This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c.
2017-08-06Merge branch 'master' into core-updatesMark H Weaver
2017-08-05gnu: perl: Work around more "dotless @INC" build issues.Ludovic Courtès
* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path' phase. * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment 'configure' phase to set PERL5LIB. * gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
2017-08-03gnu: bioinformatics.scm: Use (gnu packages cran) module.Efraim Flashner
This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
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