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Author SHA1 Message Date
Ricardo Wurmus
fe0b76e215
gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
 2019-03-06 21:23:42 +01:00
Ricardo Wurmus
40a6505711
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
...to here.
 2019-03-06 21:23:20 +01:00
Ricardo Wurmus
66e35ce63b
gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move
from here...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to
here.
 2019-03-06 21:16:33 +01:00
Ricardo Wurmus
bfb93b4889
gnu: r-geneplotter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here...
* gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
 2019-03-06 21:13:38 +01:00
Ricardo Wurmus
9f8698ad1c
gnu: Add guile-stis-parser. 
* gnu/packages/guile-xyz.scm (guile-stis-parser): New variable.
 2019-03-06 21:07:49 +01:00
Ricardo Wurmus
3d13b448e5
gnu: r-copynumber: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here...
* gnu/packages/bioconductor.scm (r-copynumber): ...to here.
 2019-03-06 21:07:49 +01:00
Ricardo Wurmus
6aa896d82e
gnu: Update copyright headers. 
This is a follow-up to commit 1fe9a36173.

* gnu/packages/bioconductor.scm: Update copyright header to account for moved
package.
 2019-03-06 21:07:49 +01:00
Efraim Flashner
d2b38df62e
gnu: font-gnu-unifont: Update to 12.0.01. 
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 12.0.01.
 2019-03-06 20:51:47 +02:00
Tobias Geerinckx-Rice
393b55d5c7
gnu: cabextract: Don't use NAME in source URI. 
* gnu/packages/compression.scm (cabextract)[source]: Hard-code NAME.
 2019-03-06 16:48:40 +01:00
Tobias Geerinckx-Rice
bde093c23d
gnu: cabextract: Update to 1.9.1. 
* gnu/packages/compression.scm (cabextract): Update to 1.9.1.
 2019-03-06 16:48:39 +01:00
Tobias Geerinckx-Rice
8fadbc4bb3
gnu: lcov: Update to 1.14. 
* gnu/packages/code.scm (lcov): Update to 1.14.
 2019-03-06 16:48:39 +01:00
Marius Bakke
7016e62070
gnu: python-mako: Update home page. 
* gnu/packages/python-xyz.scm (python-mako)[home-page]: Use HTTPS.
 2019-03-06 16:30:48 +01:00
Marius Bakke
dff79364cf
gnu: fuseiso: Fix typo. 
* gnu/packages/linux.scm (fuseiso)[synopsis]: s/imsages/images.
 2019-03-06 16:30:48 +01:00
Marius Bakke
a9eeda20b4
gnu: valgrind: Add download mirror. 
* gnu/packages/valgrind.scm (valgrind)[source](uri): Add mirror.
 2019-03-06 16:30:48 +01:00
Ricardo Wurmus
38502a7d13
gnu: bismark: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1.
[source]: Remove obsolete snippet.
[arguments]: Add build phase "replace-plotly.js" and add requried modules;
adjust "install" phase.
[inputs]: Add perl-carp and perl-getopt-long.
[native-inputs]: Add plotly.js and uglify-js.
 2019-03-06 16:26:23 +01:00
Pierre Neidhardt
1564e0fefa
gnu: Add fuseiso. 
* gnu/packages/linux.scm (fuseiso): New variable.
 2019-03-06 16:24:34 +01:00
Ricardo Wurmus
cb66fb101f
gnu: Add r-scde. 
* gnu/packages/bioinformatics.scm (r-scde): New variable.
 2019-03-06 15:55:54 +01:00
Ricardo Wurmus
afeb10a056
gnu: Add bowtie1. 
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
 2019-03-06 15:32:45 +01:00
Kei Kebreau
5b8f892872
gnu: octave, octave-cli: Update to 5.1.0. 
* gnu/packages/maths.scm (octave, octave-cli): Update to 5.1.0.
 2019-03-06 09:17:33 -05:00
Kei Kebreau
e366521a94
gnu: crawl, crawl-tiles: Update to 0.23.1. 
* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.23.1.
[native-inputs]: Add python and python-pyyaml.
[arguments]: Add 'patch-python' phase, modify the 'check' phase and move the
'check' phase back after the 'build' phase.
 2019-03-06 09:17:24 -05:00
Ricardo Wurmus
5bb674a0cd
gnu: perl-czplib: Fix installation directory. 
* gnu/packages/perl.scm (perl-czplib)[arguments]: Fix installation directory.
 2019-03-06 15:05:38 +01:00
Ricardo Wurmus
5531782d1c
gnu: Add guile-studio. 
* gnu/packages/guile-xyz.scm (guile-studio): New variable.
 2019-03-06 14:40:02 +01:00
Ricardo Wurmus
4fc9b5b1dd
gnu: Add genrich. 
* gnu/packages/bioinformatics.scm (genrich): New variable.
 2019-03-06 13:28:45 +01:00
Ricardo Wurmus
1fe9a36173
gnu: r-dnacopy: Remove duplicate definition. 
Reported by Christopher Baines <mail@cbaines.net>.

* gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
 2019-03-06 10:39:28 +01:00
Ricardo Wurmus
3dad6087be
gnu: Add r-org-dr-eg-db. 
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): New variable.
 2019-03-06 10:29:25 +01:00
Ricardo Wurmus
43d6776ba4
gnu: java-eclipse-jdt-core: Update to 3.16.0. 
* gnu/packages/java.scm (java-eclipse-jdt-core): Update to 3.16.0.
 2019-03-06 10:10:23 +01:00
Ricardo Wurmus
c8427a5e91
gnu: java-eclipse-core-resources: Update to 3.13.200. 
* gnu/packages/java.scm (java-eclipse-core-resources): Update to 3.13.200.
 2019-03-06 10:10:23 +01:00
Ricardo Wurmus
4fa9b6e657
gnu: java-eclipse-core-runtime: Update to 3.15.100. 
* gnu/packages/java.scm (java-eclipse-core-runtime): Update to 3.15.100.
 2019-03-06 10:10:23 +01:00
Ricardo Wurmus
e40e3792e6
gnu: java-eclipse-equinox-common: Update to 3.10.200. 
* gnu/packages/java.scm (java-eclipse-equinox-common): Update to 3.10.200.
 2019-03-06 10:10:19 +01:00
Rutger Helling
d9eada7917
gnu: shaderc: Update to 2018.0. 
* gnu/packages/vulkan.scm (shaderc): Update to 2018.0.
 2019-03-06 09:26:50 +01:00
Rutger Helling
264c803b82
gnu: spirv-tools: Update to 2019.1. 
* gnu/packages/vulkan.scm (spirv-tools): Update to 2019.1.
[arguments]: Add 'fixgcc7 phase.
[native-inputs]: Add gcc-7.
 2019-03-06 09:26:50 +01:00
Rutger Helling
9a1de5f0fa
gnu: spirv-headers: Update to commit 8bea0a2. 
* gnu/packages/vulkan.scm (spirv-headers): Update to commit 8bea0a2.
 2019-03-06 09:26:49 +01:00
Rutger Helling
3113ecfaec
gnu: glslang: Update to 7.11.3113. 
* gnu/packages/vulkan.scm (glslang): Update to 7.11.3113.
 2019-03-06 09:26:49 +01:00
Leo Famulari
3546e97f38
gnu: MPD: Update to 0.21.5. 
* gnu/packages/mpd.scm (mpd): Update to 0.21.5.
 2019-03-05 21:10:54 -05:00
Arne Babenhauserheide
84eb265eb8
gnu: FFmpeg: Build with AV1 support. 
* gnu/packages/video.scm (ffmpeg)[inputs]: Add libaom.
[arguments]: Pass '--enable-libaom' to #:configure-flags.
(ffmpeg-3.4)[inputs, arguments]: Filter out libaom.
 2019-03-05 18:29:20 -05:00
Arne Babenhauserheide
a7afa45401
gnu: Add libaom. 
* gnu/packages/video.scm (libaom): New variable.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2019-03-05 18:29:20 -05:00
Tobias Geerinckx-Rice
dbfa3bb5d0
gnu: you-get: Update to 0.4.1256. 
* gnu/packages/video.scm (you-get): Update to 0.4.1256.
 2019-03-06 00:15:28 +01:00
Tobias Geerinckx-Rice
fe67e51301
gnu: youtube-dl: Update to 2019.03.01. 
* gnu/packages/video.scm (youtube-dl): Update to 2019.03.01.
 2019-03-06 00:15:27 +01:00
Tobias Geerinckx-Rice
84bdd0ec06
gnu: plantuml: Update to 1.2019.2. 
* gnu/packages/uml.scm (plantuml): Update to 1.2019.2.
 2019-03-06 00:15:27 +01:00
Tobias Geerinckx-Rice
2830802043
gnu: xinit: Update to 1.4.1. 
* gnu/packages/xorg.scm (xinit): Update to 1.4.1.
 2019-03-06 00:15:27 +01:00
Tobias Geerinckx-Rice
2e625ef73a
gnu: lxc: Fix documentation directory. 
* gnu/packages/virtualization.scm (lxc)[arguments]: Set ‘--docdir’ in #:configure-flags.
 2019-03-06 00:15:26 +01:00
Tobias Geerinckx-Rice
cc7058b20b
gnu: lxc: Update to 3.1.0. 
* gnu/packages/virtualization.scm (lxc): Update to 3.1.0.
 2019-03-06 00:15:26 +01:00
Leo Famulari
5f7c036cf6
gnu: dav1d: Update to 0.2.0. 
* gnu/packages/video.scm (dav1d): Update to 0.2.0.
[source]: Add alternate URL.
 2019-03-05 17:56:49 -05:00
Ludovic Courtès
5387971a9e
artwork: Update snapshot to b975164. 
* gnu/artwork.scm (%artwork-repository): Update to b975164.
 2019-03-05 23:08:53 +01:00
Ludovic Courtès
af85757915
gnu: singularity: Leave PATH unchanged. 
Previously 'singularity help' & co. would all fail on Guix System
because Coreutils, grep, etc. were not found in $PATH.

* gnu/packages/linux.scm (singularity)[source](snippet): Remove "PATH"
setting from 'bin/singularity.in'.
 2019-03-05 23:08:53 +01:00
Ludovic Courtès
fbf26cbcf3
gnu: singularity: Patch 'Makefile.in' in a snippet. 
* gnu/packages/linux.scm (singularity)[source](snippet, modules): New
fields.
[arguments]: Remove 'disable-install-hook' phase.
 2019-03-05 23:08:53 +01:00
Ludovic Courtès
107b081ef7
gnu: wpa-supplicant: Add 'cpe-name' property. 
* gnu/packages/admin.scm (wpa-supplicant-minimal)[properties]: New
field.
 2019-03-05 23:08:53 +01:00
Leo Famulari
f4319c6e28
gnu: Syncthing: Update to 1.1.0. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.1.0.
 2019-03-05 14:42:49 -05:00
Efraim Flashner
f862697b5c
gnu: emacs-no-x-toolkit: Fix configure flags. 
* gnu/packages/emacs.scm (emacs-no-x-toolkit)[arguments]: Don't lose
custom configure flags.
 2019-03-05 21:38:51 +02:00
Pierre Neidhardt
7e80767dc3
gnu: emacs-disk-usage: Update to 1.3.0. 
* gnu/packages/emacs-xyz.scm (emacs-disk-usage): Update to 1.3.0.
 2019-03-05 20:03:20 +01:00