03d6e9dd08
gnu: vsearch: Update to 2.5.2.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2.
2017-11-01 10:57:05 +10:00
e126b79736
gnu: diamond: Update to 0.9.11.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11.
2017-11-01 10:57:03 +10:00
7bf59f7021
gnu: Remove cufflinks.
...
Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946 >.
* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.
2017-10-31 08:17:06 +01:00
ed5e9a33f8
gnu: vsearch: Update to 2.5.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1.
2017-10-26 19:55:29 +10:00
6f141eff47
gnu: bwa: Update to 0.7.17.
...
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17.
2017-10-25 09:29:22 +10:00
ae6e00f6f9
gnu: bwa: Change source URL to GitHub.
...
* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to
GitHub.
2017-10-25 09:29:22 +10:00
ce4dfde0d8
gnu: miso: Update to 0.5.4.
...
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4.
2017-10-23 14:49:29 +02:00
5713bbf157
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.
2017-10-21 17:43:40 +02:00
c0770feedd
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.
2017-10-18 23:54:16 +02:00
af6ce61088
gnu: python-biopython: Update to 1.70.
...
* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.
2017-10-14 03:17:50 +02:00
dad66da493
gnu: Add plink-ng.
...
* gnu/packages/bioinformatics.scm (plink-ng): New variable.
2017-10-13 11:14:00 +02:00
dc8ddbfb07
gnu: Add paml.
...
* gnu/packages/bioinformatics.scm (paml): New variable.
2017-10-13 11:14:00 +02:00
b3936f35ae
gnu: clustal-omega: Update to 1.2.4.
...
* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.
2017-10-12 23:54:54 +02:00
c6643f2d52
gnu: f-seq: Truncate version string.
...
* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of
the version string.
2017-10-12 08:43:54 +02:00
01d87d3c18
gnu: rcas-web: Update to 0.0.4.
...
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
2017-10-11 21:37:37 +02:00
ad3a937dae
Merge branch 'master' into staging
2017-10-07 12:54:40 +02:00
3ae76f7f57
gnu: vsearch: Update to 2.5.0.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
2017-10-07 09:42:55 +10:00
ffcff27272
Merge branch 'master' into staging
2017-09-24 19:18:35 +02:00
8c864901b6
gnu: proteinortho: Update to 5.16b.
...
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
2017-09-23 18:10:14 +10:00
9fc513ad10
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.
2017-09-22 12:21:09 +02:00
dc1d3cdef7
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.
2017-09-20 20:58:04 -04:00
ebfd6a718a
gnu: r-rcas: Add missing inputs.
...
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
2017-09-18 14:23:03 +02:00
d82937fbe0
gnu: r-rcas: Update to 1.3.4.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
2017-09-18 11:33:26 +02:00
4561498e1f
gnu: Fix build failures caused by commit
...
d10092b849
2017-09-10 18:21:35 -04:00
325c039c1d
gnu: Add r-sparql.
...
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
2017-09-05 11:02:03 +02:00
d10092b849
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.
2017-09-04 00:10:59 -04:00
81195d139f
gnu: r-genomicalignments: Update to 1.12.2.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
2017-09-01 15:11:58 +02:00
db2e43863c
gnu: r-vegan: Update to 2.4-4.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.
2017-09-01 15:11:57 +02:00
7b92acdf52
gnu: r-maldiquant: Update to 1.16.4.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
2017-09-01 15:11:57 +02:00
6bd27981f6
gnu: r-bookdown: Update to 0.5.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
2017-09-01 15:11:56 +02:00
75690c9f6b
gnu: r-rcas: Correct license.
...
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01 10:26:31 +02:00
eda8f36cd6
gnu: r-rcas: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
2017-09-01 10:26:30 +02:00
f4bf420c84
gnu: vsearch: Update to 2.4.4.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
2017-09-01 14:45:57 +08:00
25bd1fc1c1
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.
2017-09-01 14:45:57 +08:00
0691851a64
gnu: bioinformatics: Work around more "dotless @INC" build failures.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
2017-08-31 12:37:05 +08:00
690a904ad7
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.
2017-08-31 10:43:18 +08:00
799247d2d9
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.
2017-08-30 17:32:00 +02:00
2718a9cd09
Merge branch 'master' into core-updates
2017-08-21 02:40:37 +02:00
17cddc1714
gnu: Add r-annotationfilter.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-08-20 14:00:04 +02:00
bf3fa99654
gnu: Add r-methylkit.
...
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
2017-08-17 18:00:17 +02:00
212f612040
gnu: Add r-qvalue.
...
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
2017-08-17 17:26:12 +02:00
d4a1e918cb
gnu: Add r-fastseg.
...
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
2017-08-17 17:26:11 +02:00
4a007ffafe
gnu: Add r-annotationhub.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
2017-08-17 17:25:47 +02:00
5f96f30f5d
gnu: Add r-interactivedisplaybase.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
2017-08-17 17:25:46 +02:00
d534f3a4d3
gnu: r-mzr: Fix building on aarch64 and armhf.
...
* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
2017-08-16 12:36:25 +03:00
06f31e50b1
gnu: diamond: Update to 0.9.10.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
2017-08-15 18:49:33 +10:00
3837108e40
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.
2017-08-15 10:31:20 +03:00
09ec5a0f0c
Merge branch 'master' into core-updates
2017-08-15 03:10:14 -04:00
9634804890
gnu: Add bismark.
...
* gnu/packages/bioinformatics.scm (bismark): New variable.
2017-08-14 12:00:56 +02:00
86763fdd70
gnu: Add r-dexseq.
...
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
2017-08-14 12:00:51 +02:00
Ben Woodcroft