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Author SHA1 Message Date
Ricardo Wurmus
6b31040ae6
gnu: python-py2bit: Update to 0.3.0. 
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
6b7260bad1
gnu: cutadapt: Update to 1.18. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
a5b0038cbd
gnu: Add python-dnaio. 
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
7321920cd3
gnu: crossmap: Update to 0.2.9. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
8640f9ec91
gnu: python-twobitreader: Update to 3.1.6. 
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
f5cec0068a
gnu: Add python-bx-python. 
* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
2ba2d62c69
gnu: python2-bx-python: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2.
[source]: Remove obsolete snippet.
[inputs]: Move python2-numpy from here...
[propagated-inputs]: ...to here; add python2-six.
[native-inputs]: Add python2-lzo and python2-cython.
[home-page]: Update to new home at Github.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
1d18ee6dfd
gnu: bwa-pssm: Fetch from git. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus
9a6808e0c0
gnu: tophat: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-10-21 23:06:45 +02:00
Mark H Weaver
f7618bf18e
gnu: linux-libre: Update to 4.18.16. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16.
(%linux-libre-hash): Update hash.
 2018-10-21 14:59:30 -04:00
Mark H Weaver
668834cae0
gnu: linux-libre@4.14: Update to 4.14.78. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78.
(%linux-libre-4.14-hash): Update hash.
 2018-10-21 14:58:03 -04:00
Mark H Weaver
c4a7a51292
gnu: linux-libre@4.9: Update to 4.9.135. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135.
 2018-10-21 14:57:24 -04:00
Mark H Weaver
9ab6c680ba
gnu: linux-libre@4.4: Update to 4.4.162. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162.
 2018-10-21 14:56:44 -04:00
Pierre Neidhardt
673364cd3a
gnu: Add emacs-slime-repl-ansi-color. 
* gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable.
 2018-10-21 19:49:10 +02:00
Marius Bakke
3a69b59332
gnu: rng-tools: Update to 6.6. 
* gnu/packages/linux.scm (rng-tools): Update to 6.6.
 2018-10-21 17:57:01 +02:00
Marius Bakke
9b6dc31b6d
gnu: fluidsynth: Update to 2.0.1. 
* gnu/packages/audio.scm (fluidsynth): Update to 2.0.1.
(fluidsynth-1): New public variable.
* gnu/packages/games.scm (gzdoom)[inputs]: Change FLUIDSYNTH to FLUIDSYNTH-1.
* gnu/packages/music.scm (lmms)[inputs]: Likewise.
 2018-10-21 17:57:01 +02:00
Marius Bakke
b6b3e5120a
gnu: libgxps: Update to 0.3.0. 
* gnu/packages/gnome.scm (libgxps): Update to 0.3.0.
[source](patches): Remove.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[inputs]: Change LIBJPEG to LIBJPEG-TURBO.
* gnu/packages/patches/libgxps-CVE-2017-11590.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2018-10-21 17:57:01 +02:00
Marius Bakke
c8d62d936e
gnu: libgxps: Propagate required inputs. 
* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ...
[propagated-inputs]: ... here.  New field.
 2018-10-21 17:57:01 +02:00
Marius Bakke
920de4286a
gnu: re2: Update to 2018-10-01. 
* gnu/packages/regex.scm (re2): Update to 2018-10-01.
 2018-10-21 17:57:01 +02:00
Marius Bakke
ab5e4be647
gnu: libgphoto2: Update to 2.5.19. 
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
 2018-10-21 17:57:01 +02:00
Marius Bakke
8941b4ab3d
gnu: appstream-glib: Update to 0.7.14. 
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
 2018-10-21 17:57:00 +02:00
Marius Bakke
8eadc55202
gnu: openal: Update to 1.19.1. 
* gnu/packages/audio.scm (openal): Update to 1.19.1.
 2018-10-21 17:57:00 +02:00
Efraim Flashner
2c17bd7b29
gnu: kodi: Disable version checker. 
Fixes bug#32997.

* gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove
the version checking configuration option.
 2018-10-21 16:39:26 +03:00
Ben Woodcroft
617c478506
gnu: python2-dendropy: Disable failing test. 
* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
 2018-10-21 22:31:56 +10:00
Ricardo Wurmus
21c837405a
gnu: bowtie: Update to 2.3.4.3. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus
f45093429c
gnu: blast+: Use INVOKE and return #T unconditionally. 
* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus
f8b697a385
gnu: bedops: Update to 2.4.35. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus
337d72fb44
gnu: bedops: Use INVOKE. 
* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus
c793f4d8fb
gnu: bamm: Fetch from git and use INVOKE. 
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus
95758e2faf
gnu: aragorn: Use invoke and simplify. 
* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus
8b4102b903
gnu: clipper: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus
895cf8278a
gnu: python-pybedtools: Update to 0.7.10. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus
129363b762
gnu: Add bedtools-2.26. 
* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
 2018-10-20 23:37:28 +02:00
Kei Kebreau
bfa47f14b1
gnu: cataclysm-dda: Update snapshot. 
* gnu/packages/games.scm (cataclysm-dda): Update snapshot to 0b2c194e5.
 2018-10-20 14:38:45 -04:00
Kei Kebreau
82cbe4e046
gnu: maxima: Update to 5.42.0. 
* gnu/packages/maths.scm (maxima): Update to 5.42.0.
 2018-10-20 14:38:45 -04:00
Oleg Pykhalov
227da3a4c5
gnu: python-glances: Update to 3.0.2. 
* gnu/packages/python.scm (python-glances): Update to 3.0.2.
 2018-10-20 18:24:23 +03:00
Oleg Pykhalov
67fd64a490
gnu: emacs-hy-mode: Update to 1.0.3. 
* gnu/packages/emacs.scm (emacs-hy-mode): Update to 1.0.3.
 2018-10-20 17:48:58 +03:00
Oleg Pykhalov
e661dca879
gnu: emacs-erc-hl-nicks: Update to 1.3.3. 
* gnu/packages/emacs.scm (emacs-erc-hl-nicks): Update to 1.3.3.
 2018-10-20 17:48:49 +03:00
Oleg Pykhalov
91c5e6a69d
gnu: emacs-yasnippet: Update to 0.13.0. 
* gnu/packages/emacs.scm (emacs-yasnippet): Update to 0.13.0.
 2018-10-20 17:48:36 +03:00
Oleg Pykhalov
292d637b9e
gnu: emacs-nginx-mode: Update to 1.1.9. 
* gnu/packages/emacs.scm (emacs-nginx-mode): Update to 1.1.9.
 2018-10-20 17:48:28 +03:00
Oleg Pykhalov
2f1dacc281
gnu: emacs-rainbow-mode: Update to 1.0.1. 
* gnu/packages/emacs.scm (emacs-rainbow-mode): Update to 1.0.1.
 2018-10-20 17:48:07 +03:00
Oleg Pykhalov
45dcdf5349
gnu: emacs-smart-mode-line: Update to 2.12.0. 
* gnu/packages/emacs.scm (emacs-smart-mode-line): Update to 2.12.0.
 2018-10-20 17:47:46 +03:00
Oleg Pykhalov
9137596179
gnu: emacs-fill-column-indicator: Update to 1.89. 
* gnu/packages/emacs.scm (emacs-fill-column-indicator): Update to 1.89.
 2018-10-20 17:47:13 +03:00
Oleg Pykhalov
83246854f3
gnu: emacs-ggtags: Update to 0.8.13. 
* gnu/packages/emacs.scm (emacs-ggtags): Update to 0.8.13.
 2018-10-20 17:46:43 +03:00
Oleg Pykhalov
42f9ebdc77
gnu: emacs-which-key: Update to 3.3.0. 
* gnu/packages/emacs.scm (emacs-which-key): Update to 3.3.0.
 2018-10-20 17:37:32 +03:00
Christopher Baines
0d3f170864
gnu: Add soundconverter. 
* gnu/packages/gnome.scm (soundconverter): New variable.
* gnu/packages/patches/soundconverter-remove-gconf-dependency.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-10-20 12:24:50 +01:00
nixo
b5a927b3ba
gnu: Add enchive. 
* gnu/packages/crypto.scm (enchive): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-10-19 23:39:41 +02:00
Ludovic Courtès
64791eb7e1
services: ntp: Document 'ntp-service-type' and 'ntp-configuration'. 
* gnu/services/networking.scm (<ntp-configuration>)[servers]: Add
default value.
(ntp-service-type)[default-value]: New field.
(ntp-service): Mark as deprecated.
* gnu/services/desktop.scm (%desktop-services): Use (service
ntp-service-type) instead of calling 'ntp-service'.
* doc/guix.texi (Networking Services): Document 'ntp-service-type' and
'ntp-configuration'.
 2018-10-19 23:39:41 +02:00
Meiyo Peng
bc83b2e22f
gnu: Add i3blocks. 
* gnu/packages/wm.scm (i3blocks): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-10-19 23:39:37 +02:00
Ricardo Wurmus
cdb84eb0e6
gnu: qsynth: Update to 0.5.3. 
* gnu/packages/audio.scm (qsynth): Update to 0.5.3.
 2018-10-19 21:59:28 +02:00