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Author SHA1 Message Date
Ricardo Wurmus 78eff85770
gnu: ams-lv2: Fetch sources from git. 
* gnu/packages/music.scm (ams-lv2)[source]: Fetch from git.
 2018-11-10 23:29:25 +01:00
Ricardo Wurmus 57906fad59
gnu: portmidi-for-extempore: Fetch sources from git. 
* gnu/packages/music.scm (portmidi-for-extempore)[source]: Fetch from git.
 2018-11-10 23:29:25 +01:00
Ricardo Wurmus ca364e7a3c
gnu: jalv-select: Fetch sources from git. 
* gnu/packages/music.scm (jalv-select)[source]: Fetch from git.
[arguments]: Add phase make-manpages-writable.
 2018-11-10 23:29:25 +01:00
Nicolas Goaziou 79b8341292
gnu: emacs-circe: Update to 2.10. 
* gnu/packages/emacs.scm (emacs-circe): Update to 2.10.
 2018-11-10 23:27:05 +01:00
Ricardo Wurmus 74c903edab
Add missing license import. 
* gnu/packages/mail.scm: Import agpl3+.
 2018-11-10 22:37:07 +01:00
Ricardo Wurmus e3a4703174
gnu: Add mumi. 
* gnu/packages/mail.scm (mumi): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 2d900b0464
gnu: Add guile-debbugs-next. 
* gnu/packages/guile.scm (guile-debbugs-next): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 7453785624
gnu: Add guile-email. 
* gnu/packages/guile.scm (guile-email): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 95906eee18
gnu: guile-ics: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guile-ics)[arguments]: Remove.
 2018-11-10 22:36:13 +01:00
Efraim Flashner e8b9aaf0b1
mtd-utils: Update to 2.0.2. 
* gnu/packages/linux.scm (mtd-utils): Update to 2.0.2.
[arguments]: Remove 'test-target, 'make-flags. Re-enable 'configure
phase. Add 'configure-flag for the unit-tests.
[native-inputs]: Add cmocka, pkg-config.
 2018-11-10 20:54:34 +02:00
Clément Lassieur a7553a7360
services: dovecot: Set correct default value for the "auth" service. 
* gnu/services/mail.scm (dovecot-configuration): Set 'service-count' to 0 for
the "auth" service.
 2018-11-10 19:12:21 +01:00
Clément Lassieur be8dd4a5fe
services: dovecot: Allow to set 'process-limit'. 
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[process-limit]: New field.
(dovecot-configuration)[services]: Set 'process-limit' to its correct default
value.
 2018-11-10 19:12:18 +01:00
Clément Lassieur 8d9bb4b4d0
services: dovecot: Allow to set 'client-limit'. 
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[client-limit]: New field.
(dovecot-configuration)[services]: Set 'client-limit' to its correct default
value.
 2018-11-10 19:12:14 +01:00
Efraim Flashner 005ec8d09c
gnu: f2fs-tools: Update to 1.11.0. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
 2018-11-10 19:29:05 +02:00
Ricardo Wurmus 03a415365a
gnu: r-ensembldb: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
 2018-11-09 19:41:54 +01:00
Ricardo Wurmus 88514b9124
gnu: r-biostrings: Update to 2.50.1. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 77bea84ba1
gnu: r-biocviews: Update to 1.50.5. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 317f5a5a91
gnu: r-sn: Update to 1.5-3. 
* gnu/packages/statistics.scm (r-sn): Update to 1.5-3.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 5174f06b0c
gnu: r-rgooglemaps: Update to 1.4.3. 
* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.3.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 492ec49890
gnu: r-tmb: Update to 1.7.15. 
* gnu/packages/cran.scm (r-tmb): Update to 1.7.15.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus fccb24501a
gnu: r-jomo: Update to 2.6-5. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-5.
[propagated-inputs]: Add r-mass.
 2018-11-09 19:41:50 +01:00
Ricardo Wurmus f87a18e660
gnu: r-rcpp: Update to 1.0.0. 
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.0.
[native-inputs]: Add r-knitr.
 2018-11-09 19:01:42 +01:00
Ricardo Wurmus 06bc7b82f7
gnu: Add r-arm. 
* gnu/packages/cran.scm (r-arm): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus cf383cf08f
gnu: Add r-feature. 
* gnu/packages/cran.scm (r-feature): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus da256afb9e
gnu: Add r-ks. 
* gnu/packages/cran.scm (r-ks): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus 4106e6ad87
gnu: Add r-misc3d. 
* gnu/packages/cran.scm (r-misc3d): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus 213e72a18d
gnu: Add r-multicool. 
* gnu/packages/cran.scm (r-multicool): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus f338e4807f
gnu: Add r-rgl. 
* gnu/packages/cran.scm (r-rgl): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus a961ae469c
gnu: Add r-destiny. 
* gnu/packages/bioconductor.scm (r-destiny): New variable.
 2018-11-09 17:15:31 +01:00
Ricardo Wurmus ff939ef4d5
gnu: Add r-h5. 
* gnu/packages/cran.scm (r-h5): New variable.
 2018-11-09 16:57:13 +01:00
Ricardo Wurmus 3a4c6288c8
gnu: Add r-aggregation. 
* gnu/packages/cran.scm (r-aggregation): New variable.
 2018-11-09 16:57:13 +01:00
Ricardo Wurmus 8a587c89af
gnu: Add r-savr. 
* gnu/packages/bioconductor.scm (r-savr): New variable.
 2018-11-09 16:45:21 +01:00
Ricardo Wurmus cee9ab244f
gnu: r-with-tests: Update to 3.5.1. 
* gnu/packages/statistics.scm (r-with-tests): Update to 3.5.1.
 2018-11-09 14:07:26 +01:00
Ricardo Wurmus 2eaaadb4d6
gnu: r-with-tests: Use INVOKE. 
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-09 14:07:22 +01:00
Pierre Neidhardt ddd925f608
gnu: Add emacs-gtk-look. 
* gnu/packages/emacs.scm (emacs-gtk-look): New variable.
 2018-11-09 11:55:08 +01:00
Pierre Neidhardt 2cce23bfb8
gnu: Add xmlrpc-c. 
* gnu/packages/xml.scm (xmlrpc-c): New variable.
 2018-11-09 11:55:08 +01:00
Mathieu Othacehe 97f33b05ec
gnu: guile-newt: Update to revision 1. 
* gnu/packages/guile.scm (guile-newt): Update to revision 1.
 2018-11-09 19:39:14 +09:00
Ricardo Wurmus 1b12b572a5
gnu: powertabeditor: Fetch sources from git. 
* gnu/packages/music.scm (powertabeditor)[source]: Fetch from git.
 2018-11-09 08:37:53 +01:00
Ricardo Wurmus b1b82aed5d
gnu: powertabeditor: Use INVOKE. 
* gnu/packages/music.scm (powertabeditor)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-09 08:37:53 +01:00
Kei Kebreau e4b62e229e
gnu: wxmaxima: Update to 18.10.1. 
* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1.
[source]: Update URL and remove patch.
* gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-11-09 01:09:06 -05:00
Leo Famulari 41d2b7f50b
gnu: PostgreSQL 9: Update to 9.6.11 [fixes CVE-2018-16850]. 
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.11.
 2018-11-08 13:42:56 -05:00
Pierre Neidhardt 2705780f3f
gnu: Add emacs-clang-format. 
* gnu/packages/emacs.scm (emacs-clang-format): New variable.
 2018-11-08 13:08:26 +01:00
Efraim Flashner e3407254d5
gnu: kodi: Update to 18.0b5. 
* gnu/packages/kodi.scm (kodi): Update to 18.0b5.
[source]: Update snippet.
[inputs]: Add flatbuffers, fstrcmp.
(crossguid): Update to commit fef89a4174a7bf8cd99fa9154864ce9e8e3bf989.
(libdvdnav/kodi, libdvdread/kodi): Update to 6.0.0-Leia-Alpha-3.
(libdvdcss/kodi): Update to 1.4.2-Leia-Beta-5.
 2018-11-08 12:01:24 +02:00
Efraim Flashner 988b78ba28
gnu: Add fstrcmp. 
* gnu/packages/kodi.scm (fstrcmp): New variable.
 2018-11-08 12:01:20 +02:00
Stefan Stefanović ec86863113
services: elogind: Fix spelling errors of left value fields in elogind config file. 
* gnu/services/desktop.scm (elogind-configuration-file)[ini-file]:
    Fix spelling of left value fields:
    InhibitDelayMaxSecs, HoldoffTimeoutSecs, IdleActionSeconds, RemoveIpc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:35 +01:00
Luther Thompson 9870b9f7f8
gnu: python-ilinkedlist: Update to 0.3.1. 
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:26 +01:00
Vagrant Cascadian 195e081b43
gnu: Add python-pyelftools. 
* gnu/packages/python.scm (python-pyelftools):
  New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:22 +01:00
Ricardo Wurmus 69cb939ee7
gnu: libmusicbrainz: Use INVOKE. 
* gnu/packages/music.scm (libmusicbrainz)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:17:15 +01:00
Ricardo Wurmus 9ab90ead36
gnu: pd: Remove custom autoconf phase. 
* gnu/packages/music.scm (pd)[arguments]: Remove custom autoconf phase.
 2018-11-08 10:14:08 +01:00
Ricardo Wurmus 4e82946888
gnu: cmus: Fetch sources from git. 
* gnu/packages/music.scm (cmus)[source]: Fetch from git.
 2018-11-08 10:10:06 +01:00
Ricardo Wurmus ec618c2005
gnu: cmus: Use INVOKE. 
* gnu/packages/music.scm (cmus)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:09:32 +01:00
Ricardo Wurmus 9c30cba431
gnu: pcc: Use INVOKE. 
* gnu/packages/c.scm (pcc)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:08:09 +01:00
Ricardo Wurmus a1e83a9856
gnu: pplacer-scripts: Use INVOKE. 
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 10:06:35 +01:00
Ricardo Wurmus ce49fdcce9
gnu: roary: Use INVOKE. 
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 09:58:05 +01:00
Ricardo Wurmus a9542937c8
gnu: seek: Use INVOKE. 
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
 2018-11-08 09:54:22 +01:00
Ricardo Wurmus 9f527c9199
gnu: sailfish: Use INVOKE. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
 2018-11-08 09:52:46 +01:00
Ricardo Wurmus 86c6928ea3
gnu: vsearch: Update to 2.9.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
 2018-11-08 09:46:42 +01:00
Ricardo Wurmus 15c9609482
gnu: sra-tools: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
 2018-11-08 09:46:05 +01:00
Ricardo Wurmus b17333414f
gnu: plink-ng: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
 2018-11-08 09:30:59 +01:00
Ricardo Wurmus 87408854ec
gnu: ncbi-vdb: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
 2018-11-08 09:30:16 +01:00
Ricardo Wurmus 8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
 2018-11-08 09:29:58 +01:00
Ricardo Wurmus 3da3cedf76
gnu: ngs-sdk: Use INVOKE. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:15:05 +01:00
Ricardo Wurmus e78e54d029
gnu: emboss: Use INVOKE. 
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:14:09 +01:00
Ricardo Wurmus 8b685c4720
gnu: taxtastic: Use INVOKE. 
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:13:35 +01:00
Ricardo Wurmus 2e2d88539c
gnu: sra-tools: Use INVOKE. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:12:43 +01:00
Ricardo Wurmus 179416467f
gnu: muscle: Use INVOKE. 
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:11:38 +01:00
Ricardo Wurmus 0881d62f25
gnu: newick-utils: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
 2018-11-08 09:10:58 +01:00
Ricardo Wurmus e35dce0170
gnu: mash: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
 2018-11-08 09:10:20 +01:00
Ricardo Wurmus 31c41a8cfe
gnu: vsearch: Remove custom autogen phase. 
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
 2018-11-08 09:04:34 +01:00
Ricardo Wurmus c527d36f02
gnu: java-picard-1.113: Use INVOKE. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
 2018-11-08 09:02:34 +01:00
Ricardo Wurmus e438c96558
gnu: fraggenescan: Use INVOKE. 
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
 2018-11-08 08:58:46 +01:00
Ricardo Wurmus c098c49b3e
gnu: sailfish: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
 2018-11-08 08:53:54 +01:00
Ricardo Wurmus 4031e7f1ec
gnu: ngs-sdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 3398dfb764
gnu: ncbi-vdb: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus e0f1aa2d2b
gnu: tadbit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
 2018-11-08 08:53:50 +01:00
Kei Kebreau ed33049cdc
gnu: pspp: Update to 1.2.0. 
* gnu/packages/statistics.scm (pspp): Update to 1.2.0.
[inputs]: Add spread-sheet-widget.
[native-inputs]: Add autoconf, python-2, and texinfo.
 2018-11-07 17:46:25 -05:00
Kei Kebreau e2f36385d3
gnu: Add spread-sheet-widget. 
* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
 2018-11-07 17:46:25 -05:00
Ricardo Wurmus f3f34b132c
gnu: filevercmp: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 3b888065da
gnu: ritornello: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git. 
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: seqtk: Update to 1.3. 
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build. 
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Efraim Flashner b44b1f08f6
gnu: hplip: Remove bundled non-free blobs. 
This fixes <https://bugs.gnu.org/32184>.

* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2018-11-07 23:16:02 +02:00
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2. 
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Marius Bakke b31e156161
gnu: fio: Update to 3.11. 
* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
 2018-11-07 21:09:00 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
 2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
 2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
 2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
 2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL. 
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
 2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5. 
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
 2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
 2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: gemma: Update to 0.98. 
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
 2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
 2018-11-07 20:26:45 +01:00
Pierre Langlois f09e8abc5e
gnu: clementine: Build with sqlite-with-column-metadata. 
* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-11-07 14:25:07 -05:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
 2018-11-07 19:55:50 +01:00
Ricardo Wurmus 7ca49ab57a
gnu: ribodiff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
 2018-11-07 19:48:21 +01:00
Ricardo Wurmus 239716fb0b
gnu: python-biom-format: Update to 2.1.7. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
 2018-11-07 19:47:07 +01:00
Ricardo Wurmus 007a81d5cf
gnu: python-biom-format: Fetch source from git. 
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
 2018-11-07 19:10:36 +01:00
Ricardo Wurmus 383cb7b8e6
gnu: bioawk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
 2018-11-07 19:06:30 +01:00
Ricardo Wurmus 20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
 2018-11-07 18:52:46 +01:00
Ricardo Wurmus 8e58319c45
gnu: bamtools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
 2018-11-07 18:44:30 +01:00
Ricardo Wurmus 21335fdbec
gnu: ngless: Install links to required tools. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
 2018-11-07 17:19:53 +01:00
Ricardo Wurmus fff67cc8a7
gnu: prodigal: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
 2018-11-07 17:19:53 +01:00
Ludovic Courtès dcb45127e0
services: cuirass: Add 'ttl' configuration field. 
* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
 2018-11-07 16:06:42 +01:00
Ludovic Courtès 08759829cf
gnu: cuirass: Update to 0b40dca. 
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
 2018-11-07 16:06:42 +01:00
Ludovic Courtès 970c9993f1
linux-initrd: Make sure 'build-initrd' can delete files. 
Fixes <https://bugs.gnu.org/33297>.
Reported by Mark H Weaver <mhw@netris.org>.

This fixes a regression introduced in
72dc64f8f7, which made files read-only.

* gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable'
on all the files under contents/.
 2018-11-07 16:06:42 +01:00
Ricardo Wurmus 9255198423
gnu: r-mzr: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8e48d36f26
gnu: r-hdf5array: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 611a255d2b
gnu: r-rhdf5: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus a1c2bf8e54
gnu: r-rcas: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 70a3a76ba7
gnu: r-scran: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 48f2791496
gnu: r-scater: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 3c833608f3
gnu: r-beachmat: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus edb91244c3
gnu: r-qvalue: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus d055f199a9
gnu: r-hitc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8023912934
gnu: r-fithic: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 7468a76480
gnu: r-sushi: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 85b16c05e8
gnu: r-gwascat: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus d57445c9b2
gnu: r-gviz: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus da679b5202
gnu: r-ldblock: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 4b91335566
gnu: r-erma: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 220ac15e3f
gnu: r-snpstats: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 181a843143
gnu: r-gqtlbase: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus f20c766413
gnu: r-ggbio: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:15 +01:00