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Author SHA1 Message Date
Ricardo Wurmus
32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus
2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus
9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus
fd757a8f21
gnu: pigx-chipseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus
1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:54 +01:00
Mark H Weaver
9f388b1ee1
Merge branch 'master' into core-updates 2018-03-17 01:18:37 -04:00
Ricardo Wurmus
c1c9cc664b
gnu: Add pigx. 
* gnu/packages/bioinformatics.scm (pigx): New variable.
 2018-03-16 15:40:31 +01:00
Ricardo Wurmus
fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
 2018-03-16 15:40:31 +01:00
Mark H Weaver
6cbee49d66
gnu: All snippets report errors using exceptions, else return #t. 
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
 2018-03-16 09:08:31 -04:00
Ricardo Wurmus
46264c73a6
gnu: Add pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
 2018-03-16 11:15:04 +01:00
Ricardo Wurmus
b44437c549
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:01:07 +01:00
Ricardo Wurmus
80420f114c
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:00:31 +01:00
Leo Famulari
32cbbac11a
gnu: Add Diversitree. 
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
 2018-03-15 10:57:51 -04:00
Ricardo Wurmus
8c72ed923d
Merge branch 'master' into core-updates 2018-03-14 17:37:20 +01:00
Ludovic Courtès
189be331ac
build-system/gnu: Add 'bootstrap' phase. 
This factorizes what has become a widespread idiom.

* guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable.
(bootstrap): New procedure.
(%standard-phases): Add it after 'unpack'.
* guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap.
* guix/build/asdf-build-system.scm (%standard-phases/source)
(%standard-phases): Likewise.
* guix/build/cargo-build-system.scm (%standard-phases): Likewise.
* guix/build/cmake-build-system.scm (%standard-phases): Likewise.
* guix/build/dub-build-system.scm (%standard-phases): Likewise.
* guix/build/emacs-build-system.scm (%standard-phases): Likewise.
* guix/build/font-build-system.scm (%standard-phases): Likewise.
* guix/build/go-build-system.scm (%standard-phases): Likewise.
* guix/build/haskell-build-system.scm (%standard-phases): Likewise.
* guix/build/minify-build-system.scm (%standard-phases): Likewise.
* guix/build/ocaml-build-system.scm (%standard-phases): Likewise.
* guix/build/perl-build-system.scm (%standard-phases): Likewise.
* guix/build/python-build-system.scm (%standard-phases): Likewise.
* guix/build/r-build-system.scm (%standard-phases): Likewise.
* guix/build/ruby-build-system.scm (%standard-phases): Likewise.
* guix/build/scons-build-system.scm (%standard-phases): Likewise.
* guix/build/texlive-build-system.scm (%standard-phases): Likewise.
* guix/build/waf-build-system.scm (%standard-phases): Likewise.
* gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap.
(soundtouch, cuetools, bluez-alsa): Remove 'arguments'.
(cava)[arguments]: Replace 'bootstrap.
* gnu/packages/backup.scm (rdup): Remove 'bootstrap.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Replace
'bootstrap.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove
'arguments'.
* gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'.
* gnu/packages/crypto.scm (libb2): Remove #:phases.
* gnu/packages/databases.scm (guile-wiredtiger): Likewise.
* gnu/packages/debug.scm (stress-make): Remove 'bootstrap'.
* gnu/packages/documentation.scm (asciidoc): Likewise.
* gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'.
* gnu/packages/ftp.scm (weex): Remove 'arguments'.
* gnu/packages/game-development.scm (ois): Remove 'arguments'.
* gnu/packages/games.scm (pioneer): Remove 'bootstrap.
* gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap.
(arc-theme): Remove 'arguments'.
(faba-icon-theme): Remove 'bootstrap.
(arc-icon-theme): Remove 'arguments'.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/gtk.scm (guile-rsvg): Likewise.
* gnu/packages/guile.scm (mcron2): Remove 'bootstrap.
(guile-bash): Remove #:phases.
(guile-git): Remove 'bootstrap.
(guile-syntax-highlight): Remove 'arguments'.
(guile-sjson): Likewise.
* gnu/packages/java.scm (classpath-devel): Remove 'bootstrap.
* gnu/packages/kodi.scm (libdvdnav/kodi)
(libdvdread/kodi, libdvdcss/kodi): Likewise.
* gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'.
* gnu/packages/libusb.scm (hidapi): Likewise.
* gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to
'patch-stuff'; move it before 'bootstrap', without autoreconf
invocation.
(eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh'
invocation; move it before 'bootstrap.
(gpm): Replace 'bootstrap'.
(f2fs-tools): Remove 'arguments'.
(rng-tools): Remove #:phases.
* gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to
'copy-intltool-makefile'; remove "autoreconf" invocation and move before
'bootstrap'.
(libmesode): Remove 'arguments'.
(libstrophe): Likewise.
* gnu/packages/microcom.scm (microcom): Likewise.
* gnu/packages/networking.scm (libnet): Remove 'bootstrap.
* gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'.
* gnu/packages/package-management.scm (guix): Replace 'bootstrap.
* gnu/packages/sawfish.scm (librep): Remove 'arguments'.
* gnu/packages/version-control.scm (findnewest): Likewise.
* gnu/packages/video.scm (liba52, handbrake, motion): Replace
'bootstrap.
* gnu/packages/web.scm (fcgiwrap): Remove #:phases.
(tidy): Replace 'bootstrap.
(gumbo-parser): Remove #:phases.
* gnu/packages/wget.scm (wget2): Replace 'bootstrap.
* gnu/packages/wm.scm (i3lock-color): Remove #:phases.
* gnu/packages/xdisorg.scm (xclip): Likewise.
* gnu/packages/xml.scm (libxls): Replace 'bootstrap'.
* gnu/packages/xorg.scm (xf86-video-freedreno)
(xf86-video-intel): Remove #:phases.
* gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
 2018-03-11 22:04:40 +01:00
Ricardo Wurmus
fb94174fc3
gnu: Add pigx-bsseq. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus
531afc8a89
gnu: Add pigx-chipseq. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus
a539ad867d
gnu: r-rhdf5lib: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
 2018-03-09 11:40:59 +01:00
Ricardo Wurmus
22a0c65969
gnu: Add r-phangorn. 
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
 2018-03-08 23:31:56 +01:00
Ricardo Wurmus
53cc59a1d8
gnu: r-ape: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
 2018-03-08 23:31:55 +01:00
Ricardo Wurmus
84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f. 
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
 2018-03-08 18:53:49 +01:00
Ricardo Wurmus
0bdd5b8ab7
gnu: Add pigx-rnaseq. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
 2018-03-07 23:25:36 +01:00
Ricardo Wurmus
c072cf57b9
gnu: samtools: Update to 1.7. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus
727d847980
gnu: htslib: Update to 1.7. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus
e325c89076
gnu: r-rhdf5: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
 2018-03-06 16:03:04 +01:00
Efraim Flashner
da49d13710
gnu: piranha: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner
d9a069c2d9
gnu: libdivsufsort: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner
5110672474
gnu: seek: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner
b1d4026dfb
gnu: r-dropbead: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
 2018-03-04 12:05:10 +02:00
Ricardo Wurmus
1adeef3194
gnu: Add dropseq-tools. 
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
 2018-03-03 21:28:05 +01:00
Ricardo Wurmus
72299db9fe
gnu: Add java-picard-2.10.3. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
 2018-03-03 21:28:02 +01:00
Ricardo Wurmus
719fa958f3
gnu: Add java-htsjdk-2.10.1. 
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
 2018-03-03 21:27:59 +01:00
Ricardo Wurmus
9a599c17b7
gnu: Add java-htsjdk-latest. 
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
 2018-03-03 21:27:57 +01:00
Ricardo Wurmus
9ac7db1830
gnu: Add java-biojava-alignment-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
 2018-03-03 21:27:56 +01:00
Ricardo Wurmus
5528f9e8f0
gnu: Add java-biojava-phylo-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
 2018-03-03 21:27:53 +01:00
Ricardo Wurmus
e44da58c16
gnu: Add java-biojava-core-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
 2018-03-03 21:27:51 +01:00
Ricardo Wurmus
22c09c335b
gnu: Add java-biojava-alignment. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
 2018-03-03 21:27:48 +01:00
Ricardo Wurmus
b28c803708
gnu: Add java-biojava-phylo. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
 2018-03-03 21:27:46 +01:00
Ricardo Wurmus
10645b9212
gnu: Add java-forester-1.005. 
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
 2018-03-03 21:27:44 +01:00
Ricardo Wurmus
f09d16e594
gnu: Add java-forester. 
* gnu/packages/bioinformatics.scm (java-forester): New variable.
 2018-03-03 21:27:41 +01:00
Ricardo Wurmus
5fef15e506
gnu: Add java-biojava-core. 
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
 2018-03-03 21:27:36 +01:00
Ricardo Wurmus
bd975831c6
gnu: Add fastqc. 
* gnu/packages/bioinformatics.scm (fastqc): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus
3ede1550e8
gnu: cutadapt: Update to 1.16. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus
9aaf2813e2
gnu: r-scran: Update to 1.6.8. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
6a0e13906b
gnu: r-wgcna: Update to 1.63. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
61cbd49b30
gnu: r-topgo: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
535014ce60
gnu: r-genomicranges: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
eb8971b742
gnu: r-limma: Update to 3.34.9. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
22d96920d3
gnu: r-edger: Update to 3.20.9. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
99e4b11d81
gnu: r-shortread: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
b180893289
gnu: r-dexseq: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
 2018-03-01 21:28:52 +01:00
Ricardo Wurmus
65c9d25739
gnu: r-qtl: Update to 1.42-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
 2018-02-22 11:18:03 +01:00
Ricardo Wurmus
79c6af13d0
gnu: r-delayedmatrixstats: Update to 1.0.3. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus
59b2864d6c
gnu: r-scater: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus
d578278e35
gnu: r-gviz: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus
ca7855fcd2
gnu: r-gprofiler: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
8877ab432e
gnu: r-ensembldb: Update to 2.2.2. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
ebec98ae1d
gnu: r-seurat: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
3118b28644
gnu: r-qtl: Update to 1.42-7. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
824c200475
gnu: r-genomicranges: Update to 1.30.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
e8484711c6
gnu: r-getopt: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
9800f7d9e8
gnu: r-bookdown: Update to 0.7. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus
ff9d1a2f0c
Merge branch 'master' into core-updates 2018-02-18 00:39:25 +01:00
Ben Woodcroft
369eee8763
gnu: vsearch: Update to 2.7.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1.
 2018-02-17 12:44:29 +10:00
Mark H Weaver
150062f190
Merge branch 'master' into core-updates 2018-02-16 13:14:26 -05:00
Ben Woodcroft
5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Ricardo Wurmus
152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus
3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus
05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Mark H Weaver
932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Ben Woodcroft
119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Mark H Weaver
288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Ricardo Wurmus
97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
26e3e28cc9
gnu: r-seurat: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0.
[propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
53f0dea9d7
gnu: r-msnbase: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
b1f2753627
gnu: r-methylkit: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
c37b361e44
gnu: r-summarizedexperiment: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
373430672d
gnu: r-biomart: Update to 2.34.2. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
024f19c68b
gnu: r-genomicranges: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0674657908
gnu: r-limma: Update to 3.34.8. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
5fb1fee67b
gnu: r-variantannotation: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
d22abe1e5d
gnu: r-edger: Update to 3.20.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
66ae706c24
gnu: r-bookdown: Update to 0.6. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6.
[propagated-inputs]: Add r-xfun and ghc-pandoc.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
2e9da3390c
gnu: r-vegan: Update to 2.4-6. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
7f1d9bef50
gnu: Add r-scran. 
* gnu/packages/bioinformatics.scm (r-scran): New variable.
 2018-02-12 15:29:44 +01:00
Ricardo Wurmus
658ab21d2e
gnu: Add r-scater. 
* gnu/packages/bioinformatics.scm (r-scater): New variable.

Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus
6fb1dc17a3
gnu: Add r-singlecellexperiment. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus
9ec0898824
gnu: Add r-beachmat. 
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus
748e9f163a
gnu: Add r-rhdf5lib. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus
aba3e482b9
gnu: Add r-hdf5array. 
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
 2018-02-11 11:42:09 +01:00
Marius Bakke
9e94d063ab
gnu: multiqc: Update to 1.4. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.4.
[propagated-inputs]: Remove PYTHON-ENUM34.
 2018-02-07 15:34:08 +01:00
Mark H Weaver
e7ca634912
Merge branch 'master' into core-updates 2018-02-03 22:46:07 -05:00