| Age | Commit message (Expand) | Author |
|---|
| 2017-11-04 | gnu: diamond: Update to 0.9.12....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.
| Ben Woodcroft |
| 2017-11-03 | gnu: multiqc: Update to 1.3....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3.
[propagated-inputs]: Add python-enum34.
[license]: The license was changed to "GPLv3 or later" with this release.
| Ricardo Wurmus |
| 2017-11-03 | gnu: r-ape: Update to 5.0....* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.
| Ricardo Wurmus |
| 2017-11-01 | gnu: vsearch: Update to 2.5.2....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2.
| Ben Woodcroft |
| 2017-11-01 | gnu: diamond: Update to 0.9.11....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11.
| Ben Woodcroft |
| 2017-10-31 | gnu: Remove cufflinks....Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946>.
* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.
| Ricardo Wurmus |
| 2017-10-26 | gnu: vsearch: Update to 2.5.1....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1.
| Ben Woodcroft |
| 2017-10-25 | gnu: bwa: Update to 0.7.17....* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17.
| Ben Woodcroft |
| 2017-10-25 | gnu: bwa: Change source URL to GitHub....* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to
GitHub.
| Ben Woodcroft |
| 2017-10-23 | gnu: miso: Update to 0.5.4....* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4.
| Tobias Geerinckx-Rice |
| 2017-10-21 | Use HTTPS for bioconductor.org....* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
| Tobias Geerinckx-Rice |
| 2017-10-18 | gnu: f-seq: Fix location of commons-cli.jar....* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of
commons-cli.jar in the wrapper script.
| Ricardo Wurmus |
| 2017-10-14 | gnu: python-biopython: Update to 1.70....* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.
| Cyril Roelandt |
| 2017-10-13 | gnu: Add plink-ng....* gnu/packages/bioinformatics.scm (plink-ng): New variable.
| Ricardo Wurmus |
| 2017-10-13 | gnu: Add paml....* gnu/packages/bioinformatics.scm (paml): New variable.
| Ricardo Wurmus |
| 2017-10-12 | gnu: clustal-omega: Update to 1.2.4....* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.
| Ricardo Wurmus |
| 2017-10-12 | gnu: f-seq: Truncate version string....* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of
the version string.
| Ricardo Wurmus |
| 2017-10-11 | gnu: rcas-web: Update to 0.0.4....* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
| Ricardo Wurmus |
| 2017-10-07 | Merge branch 'master' into staging | Marius Bakke |
| 2017-10-07 | gnu: vsearch: Update to 2.5.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
| Ben Woodcroft |
| 2017-09-24 | Merge branch 'master' into staging | Marius Bakke |
| 2017-09-23 | gnu: proteinortho: Update to 5.16b....* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
| Ben Woodcroft |
| 2017-09-22 | gnu: Use xxd instead of vim....* 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.
| Ricardo Wurmus |
| 2017-09-20 | gnu: Use 'modify-phases' syntax....* 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.
| Kei Kebreau |
| 2017-09-18 | gnu: r-rcas: Add missing inputs....* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
| Ricardo Wurmus |
| 2017-09-18 | gnu: r-rcas: Update to 1.3.4....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
| Ricardo Wurmus |
| 2017-09-10 | gnu: Fix build failures caused by commit...d10092b849153dc27cfed0a9601fde6c7bdec918.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
| Kei Kebreau |
| 2017-09-05 | gnu: Add r-sparql....* gnu/packages/bioinformatics.scm (r-sparql): New variable.
| Roel Janssen |
| 2017-09-04 | gnu: Put autoconf-related phases immediately after the 'unpack phase....* 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.
| Kei Kebreau |
| 2017-09-01 | gnu: r-genomicalignments: Update to 1.12.2....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-vegan: Update to 2.4-4....* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-maldiquant: Update to 1.16.4....* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-bookdown: Update to 0.5....* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-rcas: Correct license....* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-rcas: Update to 1.3.3....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
| Ricardo Wurmus |
| 2017-09-01 | gnu: vsearch: Update to 2.4.4....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
| Ben Woodcroft |
| 2017-09-01 | gnu: metabat: Update to 2.12.1....* 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.
| Ben Woodcroft |
| 2017-08-31 | gnu: bioinformatics: Work around more "dotless @INC" build failures....* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
| Ben Woodcroft |
| 2017-08-31 | gnu: metabat: Update to 2.11.3....* 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.
| Ben Woodcroft |
| 2017-08-30 | gnu: multiqc: Update to 1.2....* 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.
| Ricardo Wurmus |
| 2017-08-21 | Merge branch 'master' into core-updates | Marius Bakke |
| 2017-08-20 | gnu: Add r-annotationfilter....* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-methylkit....* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-qvalue....* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-fastseg....* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-annotationhub....* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-interactivedisplaybase....* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
| Ricardo Wurmus |
| 2017-08-16 | gnu: r-mzr: Fix building on aarch64 and armhf....* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
| Efraim Flashner |
| 2017-08-15 | gnu: diamond: Update to 0.9.10....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
| Ben Woodcroft |
| 2017-08-15 | gnu: bcftools: Fix building on aarch64....* 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.
| Efraim Flashner |
