ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-15 11:25:22 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
27977 commits 1 branch 0 tags 448 MiB
Commit graph

1065 commits

Author SHA1 Message Date
Ricardo Wurmus
cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
f8068419a6
gnu: r-rsamtools: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
b719435ebb
gnu: r-biostrings: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
ca52123611
gnu: r-biobase: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
f642c0e4c7
gnu: r-limma: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
7f1bac3528
gnu: r-variantannotation: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
9e482c2069
gnu: r-iranges: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
41f0f94976
gnu: r-s4vectors: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
2167eafc1d
gnu: r-biocstyle: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
3241461670
gnu: r-biocinstaller: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
704fe4d115
gnu: r-grohmm: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
843826e262
gnu: r-shortread: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
b53755258a
gnu: r-systempiper: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
9f52e53d5d
gnu: r-gseabase: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
fad7c0c7bd
gnu: r-sva: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
91e1867972
gnu: r-methylkit: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
c126ba69db
gnu: r-copywriter: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
598dacf657
gnu: r-annotationfilter: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
e6b332d43b
gnu: r-rhdf5: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
19e8929cbd
gnu: r-tximport: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
da153b7f94
gnu: r-bamsignals: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
5c18470008
gnu: r-zlibbioc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
1d0263b44e
gnu: r-rhtslib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
c25154e5cb
gnu: r-rbgl: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
727706ad38
gnu: r-annotationforge: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
3fd010ff30
gnu: r-dexseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
0166dc07ef
gnu: r-deseq2: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
554fac74aa
gnu: r-genefilter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
2d4e887dc0
gnu: r-annotate: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
c7782c3f1f
gnu: r-biocviews: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
7373b4167a
gnu: r-bioccheck: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
 2017-11-07 08:15:27 +01:00
Ben Woodcroft
171ba2480f
gnu: diamond: Update to 0.9.12. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.
 2017-11-04 10:51:44 +10:00
Ricardo Wurmus
66865ab8ac
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.
 2017-11-03 17:18:52 +01:00
Ricardo Wurmus
b12c6a664d
gnu: r-ape: Update to 5.0. 
* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.
 2017-11-03 14:14:38 +01:00
Ben Woodcroft
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
Ben Woodcroft
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
Ricardo Wurmus
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Ricardo Wurmus
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
Cyril Roelandt
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
Ricardo Wurmus
dad66da493
gnu: Add plink-ng. 
* gnu/packages/bioinformatics.scm (plink-ng): New variable.
 2017-10-13 11:14:00 +02:00
Ricardo Wurmus
dc8ddbfb07
gnu: Add paml. 
* gnu/packages/bioinformatics.scm (paml): New variable.
 2017-10-13 11:14:00 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Marius Bakke
ad3a937dae
Merge branch 'master' into staging 2017-10-07 12:54:40 +02:00
Ben Woodcroft
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
Marius Bakke
ffcff27272
Merge branch 'master' into staging 2017-09-24 19:18:35 +02:00
Ben Woodcroft
8c864901b6
gnu: proteinortho: Update to 5.16b. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
 2017-09-23 18:10:14 +10:00
Ricardo Wurmus
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
Kei Kebreau
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Kei Kebreau
4561498e1f
gnu: Fix build failures caused by commit 
d10092b849.

* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
 2017-09-10 18:21:35 -04:00
Roel Janssen
325c039c1d
gnu: Add r-sparql. 
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
 2017-09-05 11:02:03 +02:00
Kei Kebreau
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
75690c9f6b
gnu: r-rcas: Correct license. 
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
 2017-09-01 10:26:31 +02:00
Ricardo Wurmus
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ricardo Wurmus
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
Marius Bakke
2718a9cd09
Merge branch 'master' into core-updates 2017-08-21 02:40:37 +02:00
Ricardo Wurmus
17cddc1714
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-08-20 14:00:04 +02:00
Ricardo Wurmus
bf3fa99654
gnu: Add r-methylkit. 
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
 2017-08-17 18:00:17 +02:00
Ricardo Wurmus
212f612040
gnu: Add r-qvalue. 
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
 2017-08-17 17:26:12 +02:00
Ricardo Wurmus
d4a1e918cb
gnu: Add r-fastseg. 
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
 2017-08-17 17:26:11 +02:00
Ricardo Wurmus
4a007ffafe
gnu: Add r-annotationhub. 
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
 2017-08-17 17:25:47 +02:00
Ricardo Wurmus
5f96f30f5d
gnu: Add r-interactivedisplaybase. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
 2017-08-17 17:25:46 +02:00
Efraim Flashner
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
Ben Woodcroft
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
Efraim Flashner
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
Mark H Weaver
09ec5a0f0c
Merge branch 'master' into core-updates 2017-08-15 03:10:14 -04:00
Ricardo Wurmus
9634804890
gnu: Add bismark. 
* gnu/packages/bioinformatics.scm (bismark): New variable.
 2017-08-14 12:00:56 +02:00
Ricardo Wurmus
86763fdd70
gnu: Add r-dexseq. 
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
 2017-08-14 12:00:51 +02:00
Mark H Weaver
cc294bcee6
Merge branch 'master' into core-updates 2017-08-09 17:25:31 -04:00
Ricardo Wurmus
1b22ecdac4
gnu: r-wgcna: Update to 1.61. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
18f5d2a70a
gnu: Add reference to (gnu packages graph). 
This is a follow-up to 1738138cb3.
 2017-08-09 15:43:35 +02:00
Mark H Weaver
2d9495da23
Merge branch 'master' into core-updates 2017-08-07 16:45:16 -04:00
Tobias Geerinckx-Rice
9d217d277e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash. 
* 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 fd40857938.
 2017-08-07 01:58:39 +02:00
Mark H Weaver
f167595ba1
Merge branch 'master' into core-updates 2017-08-06 00:23:20 -04:00
Ludovic Courtès
a56bf101c6
gnu: perl: Work around more "dotless @INC" build issues. 
* 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.
 2017-08-05 00:31:26 +02:00
Efraim Flashner
7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module. 
This is a follow up to a8cba9dd11.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
 2017-08-03 21:39:12 +03:00
Ricardo Wurmus
5e0de29892
gnu: r-seqminer: Update to 6.0. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
4e0c847d59
gnu: r-wgcna: Update to 1.60. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
c8a9b2bcbf
gnu: r-qtl: Update to 1.41-6. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
023aa8ff58
gnu: r-seqinr: Update to 3.4-5. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
7150f1c30c
gnu: r-optparse: Update to 1.4.4. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
3f6ec083ec
gnu: r-bookdown: Update to 0.4. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
 2017-08-03 17:53:53 +02:00
Ben Woodcroft
75e6639f36
gnu: htseq: Use PyPI URI. 
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
 2017-08-03 21:08:13 +10:00
Ben Woodcroft
92971d68ac
gnu: htseq: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
 2017-08-03 21:02:30 +10:00
Roel Janssen
f1915a5dd0
gnu: r-deseq2: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
 2017-08-02 00:33:23 +02:00
Roel Janssen
fd215c2978
gnu: r-annotationforge: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
 2017-08-02 00:33:07 +02:00
Roel Janssen
bd4a0bab5f
gnu: r-category: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
 2017-08-02 00:32:46 +02:00
Roel Janssen
0ff478344b
gnu: r-biocstyle: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
 2017-08-02 00:32:31 +02:00
Roel Janssen
9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
 2017-08-02 00:32:11 +02:00
Roel Janssen
3ec25eb2a8
gnu: r-iranges: Update to 2.10.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
 2017-08-02 00:31:46 +02:00
Roel Janssen
6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
 2017-08-02 00:31:28 +02:00
Roel Janssen
48f5d283b2
gnu: r-variantannotation: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
 2017-08-02 00:31:08 +02:00
Roel Janssen
1b4738e23c
gnu: r-limma: Update to 3.32.5. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
 2017-08-02 00:30:49 +02:00
Roel Janssen
1898a7832f
gnu: r-biobase: Update to 2.36.2. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
 2017-08-02 00:30:27 +02:00
Roel Janssen
62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
 2017-08-02 00:28:32 +02:00
Roel Janssen
0c6494a1db
gnu: r-biomart: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
 2017-08-02 00:28:16 +02:00
Roel Janssen
1ff74d074e
gnu: r-biocparallel: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
 2017-08-02 00:27:57 +02:00
Roel Janssen
5077bc3e2e
gnu: r-biostrings: Update to 2.44.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
 2017-08-02 00:27:35 +02:00
Roel Janssen
adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
 2017-08-02 00:27:16 +02:00
Roel Janssen
f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
 2017-08-02 00:26:55 +02:00
Roel Janssen
26760c80cd
gnu: r-genomicalignments: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
 2017-08-02 00:26:33 +02:00
Roel Janssen
15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
 2017-08-02 00:26:00 +02:00
Roel Janssen
8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
 2017-08-02 00:25:26 +02:00
Roel Janssen
9eb2714625
gnu: r-copywriter: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
 2017-08-02 00:25:00 +02:00
Roel Janssen
bfa0d1e773
gnu: r-sva: Update to 3.24.4. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
 2017-08-02 00:24:27 +02:00
Marius Bakke
aa9780daf9
Merge branch 'master' into core-updates 2017-08-01 23:42:28 +02:00
Efraim Flashner
d931a4bbeb
gnu: metabat: Limit to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
 2017-08-01 17:28:35 +03:00
Ben Woodcroft
a9085f0c5c
gnu: metabat: Update to 2.11.2. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
 2017-07-29 22:37:47 +10:00
Ben Woodcroft
d3dce32216
gnu: metabat: Fix boost-related compilation issue. 
Reported by Leo Famulari.

* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 22:35:52 +10:00
Ben Woodcroft
f3f68a442c
gnu: metabat: Update to 2.11.1. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft
897ab082b2
gnu: python-plastid: Update to 0.4.8. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft
0620387a59
gnu: bcftools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag.  Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft
63fa0ffcd4
gnu: samtools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft
4fb6d1280e
gnu: htslib: Update to 1.5. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft
60739965da
gnu: python-pysam: Update to 0.11.2.2. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft
bca2c57658
gnu: bamm: Use htslib-1.3. 
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft
98593f9f51
gnu: bcftools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch.  Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft
4ab1644049
gnu: samtools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
 2017-07-23 10:29:34 +10:00
Ben Woodcroft
a9e4a1e641
gnu: htslib: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
 2017-07-23 10:29:34 +10:00
Ben Woodcroft
c842d42593
gnu: samtools: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
 2017-07-23 10:29:34 +10:00
Ricardo Wurmus
3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
 2017-07-22 17:31:19 +02:00
Ricardo Wurmus
a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
 2017-07-22 17:22:07 +02:00
Ricardo Wurmus
fd40857938
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
 2017-07-19 14:39:37 +02:00
Efraim Flashner
2324541bd0
gnu: sortmerna: Limit support to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
 2017-07-19 14:37:47 +03:00
Efraim Flashner
2805f9b2a0
gnu: raxml: Limit to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
 2017-07-18 09:00:10 +03:00
Ben Woodcroft
06e372360e
gnu: bowtie: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
 2017-07-14 19:23:37 +10:00
Ben Woodcroft
d6e63cf31c
gnu: bowtie: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
 2017-07-14 18:54:10 +10:00
Ricardo Wurmus
fed7200862
gnu: deeptools: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
 2017-07-09 17:07:27 +02:00
Ricardo Wurmus
eb2200f3bd
gnu: Add python-py2bit. 
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
 2017-07-09 17:07:23 +02:00
Ben Woodcroft
4732e6ee84
gnu: blast+: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.  Add patch.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-08 12:05:59 +10:00
Leo Famulari
0a66c38764
Revert "gnu: blast+: Update to 2.6.0." 
This reverts commit 18dea67dc3.
 2017-07-06 19:38:55 -04:00
Efraim Flashner
ce7e361fa3
gnu: gemma: Fix building on non-Intel architectures. 
* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
 2017-07-04 22:55:44 +03:00
Ben J Woodcroft
a522517cdb
gnu: diamond: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
 2017-07-04 19:59:01 +10:00
Ben Woodcroft
18dea67dc3
gnu: blast+: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.
 2017-07-04 19:58:42 +10:00
Ben Woodcroft
ba773f65f0
gnu: cd-hit: Update to 4.6.8. 
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
 2017-07-01 10:49:37 +10:00
Ben Woodcroft
fd99d95b3f
gnu: bwa: Update to 0.7.15. 
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
 2017-07-01 09:48:20 +10:00
Ricardo Wurmus
7ceb0a83e3
gnu: Add f-seq. 
* gnu/packages/bioinformatics.scm (f-seq): New variable.
 2017-06-25 22:26:07 +02:00
Ben Woodcroft
dfc83eadaf
gnu: orfm: Update to 0.7.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
 2017-06-24 14:46:46 +10:00
Ben Woodcroft
ab8d728144
gnu: orfm: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
 2017-06-23 22:22:50 +10:00
Ricardo Wurmus
94820951d6
gnu: Add kentutils. 
* gnu/packages/bioinformatics.scm (kentutils): New variable.
 2017-06-23 08:09:33 +02:00
Ricardo Wurmus
c1dfe8c30b
gnu: python2-bx-python: Update to 0.7.3. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
 2017-06-22 17:25:40 +02:00
Arun Isaac
148585c240
gnu: Move contents of zip module into compression module. 
* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
 2017-06-20 18:10:35 +05:30
Ben Woodcroft
0002be1d0b
gnu: diamond: Update to 0.9.8. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
 2017-06-17 13:05:08 +10:00
Tobias Geerinckx-Rice
a147fadd3b
gnu: tadbit: Fix typo in description. 
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
 2017-06-16 00:29:21 +02:00
Efraim Flashner
07bf6929b9
gnu: gemma: Fix indentation. 
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
 2017-06-15 10:32:03 +03:00
Efraim Flashner
2c9232ae69
gnu: gemma: Fix building on 32-bit architectures. 
* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
 2017-06-15 10:31:44 +03:00
Ricardo Wurmus
8befd0940b
gnu: Add tadbit. 
* gnu/packages/bioinformatics.scm (tadbit): New variable.
 2017-06-09 03:32:23 +02:00
Ricardo Wurmus
aa163424b2
gnu: Add imp. 
* gnu/packages/bioinformatics.scm (imp): New variable.
 2017-06-09 03:31:51 +02:00
Ricardo Wurmus
282b01515b
gnu: Add phylip. 
* gnu/packages/bioinformatics.scm (phylip): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus
3420c905cd
gnu: Add gess. 
* gnu/packages/bioinformatics.scm (gess): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus
44f6c88909
gnu: Add trim-galore. 
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus
b8fffd3a53
gnu: Add ritornello. 
* gnu/packages/bioinformatics.scm (ritornello): New variable.
 2017-06-09 03:31:50 +02:00
Ben Woodcroft
f69ff11af7
gnu: diamond: Update to 0.9.6. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
 2017-06-08 09:39:23 +10:00
Roel Janssen
b9a601d9db
gnu: Add kaiju. 
* gnu/packages/bioinformatics.scm (kaiju): New variable.
 2017-06-02 12:38:23 +02:00
Ben Woodcroft
0d2b2fd4f4
gnu: diamond: Update to 0.9.3. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
 2017-05-28 21:06:06 -04:00
Ben Woodcroft
ca40d4e7c5
gnu: diamond: Update to 0.9.2. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
 2017-05-27 22:03:00 -04:00
Ben Woodcroft
b608765a2c
gnu: diamond: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
 2017-05-22 21:17:41 +01:00
Ricardo Wurmus
296b3c631c
gnu: Add r-edaseq. 
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus
7b46532779
gnu: Add r-deseq. 
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus
d4b83651d1
gnu: Add r-aroma-light. 
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
 2017-05-22 18:54:58 +02:00
Ben Woodcroft
74297231be
gnu: fraggenescan: Update to 1.30. 
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure.  Add new test
case.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft
7569613076
gnu: roary: Update to 3.8.2. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft
3cbfc149c3
gnu: taxtastic: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
 2017-05-22 11:44:19 +01:00
Roel Janssen
b458413721
gnu: r-mutationalpatterns: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
 2017-05-22 09:44:08 +02:00
Ben Woodcroft
ef81341f0e
gnu: diamond: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
 2017-05-21 16:08:03 +01:00
Ben Woodcroft
88682c9a72
gnu: fasttree: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
 2017-05-21 15:42:08 +01:00
Ben Woodcroft
abc08cbae6
gnu: python-biom-format: Update to 2.1.6. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
 2017-05-21 15:42:08 +01:00
Pjotr Prins
2b18ad054c
gnu: Add gemma. 
* gnu/packages/bioinformatics.scm (gemma): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-05-18 14:22:03 +02:00
Ludovic Courtès
2252f087d4
gnu: guile-json: Rename "guile2.2-json" to "guile-json". 
* gnu/packages/guile.scm (guile-json)[native-inputs]: Change GUILE-2.0
to GUILE-2.2.
(guile2.2-json): Define using 'deprecated-package'.
(guile2.0-json): New variable.
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Update accordingly.
* gnu/packages/ci.scm (cuirass)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix)[inputs]: Likewise.
 2017-05-13 22:25:22 +02:00
Ben Woodcroft
c033f5d6b5
gnu: Add pplacer. 
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
 2017-05-10 22:13:55 +02:00
Ben Woodcroft
ad0ae297d4
gnu: Add taxtastic. 
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
 2017-05-10 22:13:55 +02:00
Petter
2f3108ad03
gnu: Avoid circular dependencies by Perl license. 
* guix/licenses.scm (perl-license): New variable.
* gnu/packages/bioinformatics.scm: Change (package-license perl) to perl-license.
* gnu/packages/compression.scm: Same.
* gnu/packages/databases.scm: Same.
* gnu/packages/gd.scm: Same.
* gnu/packages/language.scm: Same.
* gnu/packages/libevent.scm: Same.
* gnu/packages/mail.scm: Same.
* gnu/packages/messaging.scm: Same.
* gnu/packages/ncurses.scm: Same.
* gnu/packages/networking.scm: Same.
* gnu/packages/photo.scm: Same.
* gnu/packages/tcl.scm: Same.
* gnu/packages/tex.scm: Same.
* gnu/packages/tls.scm: Same.
* gnu/packages/web.scm: Same.
* gnu/packages/wm.scm: Same.
* gnu/packages/xml.scm: Same.
* gnu/packages/xorg.scm: Same.
* gnu/packages/zip.scm: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-05-02 23:41:14 +02:00
Roel Janssen
f432254237
gnu: vcftools: Update to 0.1.15. 
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
 2017-05-01 16:18:39 +02:00
Efraim Flashner
90f83099e8
gnu: r-genomeinfodbdata: Fix source url. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use
source uri and not bioconductor-uri shortener.
 2017-04-29 22:53:43 +03:00
Roel Janssen
524bfe2dbf
gnu: r-msnid: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
 2017-04-28 11:05:42 +02:00
Roel Janssen
82359c72cb
gnu: r-msnbase: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
 2017-04-28 11:05:41 +02:00
Roel Janssen
5bfa6e090d
gnu: r-pcamethods: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
 2017-04-28 11:05:40 +02:00