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Author SHA1 Message Date
Efraim Flashner
5a4aab2193
gnu: Add r-qtl2. 
* gnu/packages/bioinformatics.scm (r-qtl2): New variable.
 2019-12-10 13:11:44 +02:00
Pierre Neidhardt
88f06fd015
gnu: Really move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm. 
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
  javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
  javascript module instead of lisp.
 2019-12-05 16:23:06 +01:00
Tobias Geerinckx-Rice
d9544d91a6
Revert "gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm." 
This reverts commit ac1ee30f4f, which
still breaks ‘guix pull’.
 2019-12-05 15:38:52 +01:00
Pierre Neidhardt
ac1ee30f4f
gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm. 
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
  javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
  javascript module instead of lisp.
 2019-12-05 13:48:47 +01:00
Marius Bakke
33b59c1a3e
Merge branch 'staging' 2019-12-04 20:12:41 +01:00
Ricardo Wurmus
ec1224a73b
gnu: python-scipy: Move to (gnu packages python-science). 
* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from
here...
* gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here.
* gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm,
gnu/packages/statistics.scm: Adjust module imports.
 2019-12-02 15:25:17 +01:00
Ricardo Wurmus
076527c354
Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm." 
This reverts commit abf43a67d5 as it broke "guix pull".
 2019-11-28 21:09:24 +01:00
Pierre Neidhardt
abf43a67d5
gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm. 
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
  javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
 2019-11-28 19:36:12 +01:00
Marius Bakke
0897ad7fac
Merge branch 'master' into staging 2019-11-28 00:38:25 +01:00
Efraim Flashner
3546771cc8
gnu: libdivsufsort: Move to datastructures.scm. 
* gnu/packages/bioinformatics.scm (libdivsufsort): Move to ...
* gnu/packages/datastructures.scm: ... here.
 2019-11-25 14:08:32 +02:00
Efraim Flashner
8b1fd3cafd
gnu: bioperl-minimal: Don't use unstable tarball. 
* gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download
using git-fetch.
 2019-11-25 14:08:31 +02:00
Marius Bakke
b60d2bfff9
Merge branch 'master' into staging 2019-11-21 22:44:15 +01:00
Timothy Sample
c1637311b6
gnu: ngless: Update to 1.0.1. 
* gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1.
[arguments]: Add a 'create-Versions.hs' phase that patches the Makefile
and invokes 'make' to generate a required file.
[inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and
'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib',
'ghc-diagrams-svg', and 'ghc-tar-conduit'.
 2019-11-20 20:48:54 -05:00
Marius Bakke
f056553c6b
Merge branch 'master' into staging 2019-11-15 20:11:35 +01:00
Ricardo Wurmus
4dcf32b56b
gnu: r-gprofiler: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
 2019-11-14 10:14:10 +01:00
Efraim Flashner
f1d4d79fb3
gnu: Add 'file-name' where appropriate. 
* gnu/packages/admin.scm (detox, neofetch),
gnu/packages/algebra.scm (python-fpylll),
gnu/packages/bioinformatics.scm (tbsp, genrich),
gnu/packages/crypto.scm (hpenc),
gnu/packages/digest.scm (xxhash),
gnu/packages/emacs-xyz.scm (emacs-tiny, emacs-ergoemacs-mode,
emacs-make-it-so, emacs-poet-theme, emacs-deft, emacs-scribble-mode,
emacs-helm-mu, emacs-unidecode, emacs-diff-hl, emacs-helm-exwm,
emacs-gif-screencast, emacs-exec-path-from-shell),
gnu/packages/engineering.scm (gpx),
gnu/packages/freedesktop.scm (waylandpp),
gnu/packages/golang.scm (go-github-com-sirupsen-logrus,
go-github-com-shirou-gopsutil),
gnu/packages/guile-xyz.scm (guile-studio, guile-picture-language,
jupyter-guile-kernel),
gnu/packages/image-viewers.scm (qview),
gnu/packages/java-maths.scm (java-jblas),
gnu/packages/llvm.scm (libclc),
gnu/packages/logging.scm (spdlog),
gnu/packages/ocaml.scm (ocaml-cstruct, ocaml-zarith),
gnu/packages/terminals.scm (libtsm),
gnu/packages/tigervnc.scm (tigervnc-client),
gnu/packages/xdisorg.scm (xcalib, xbanish) [source]: Add file-name.
 2019-11-10 12:42:10 +02:00
Marius Bakke
023522d3a1
Merge branch 'master' into staging 2019-10-21 00:33:43 +02:00
Marius Bakke
0fe041bd9f
gnu: Remove more GCC < 7 workarounds. 
* gnu/packages/abiword.scm (abiword)[arguments]: Do not pass "-std=c++11" to
the GCC command line.
* gnu/packages/aidc.scm (zbar)[arguments]: Likewise.
* gnu/packages/android.scm (android-libbase, android-libcutils,
android-libziparchive, fastboot)[arguments]: Likewise.
* gnu/packages/audio.scm (azr3, guitarix, suil)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bless)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Likewise.
* gnu/packages/code.scm (rtags)[arguments]: Likewise.
* gnu/packages/coq.scm (coq-gappa)[arguments]: Likewise.
* gnu/packages/emulators.scm (dolphin-emu)[arguments]: Likewise.
* gnu/packages/engineering.scm (xyce-serial, xyce-parallel)[arguments]: Likewise.
* gnu/packages/gnupg.scm (pinentry-qt)[arguments]: Likewise.
* gnu/packages/gobby.scm (libnet6, obby)[arguments]: Likewise.
* gnu/packages/graph.scm (python-faiss)[arguments]: Likewise.
* gnu/packages/graphics.scm (povray)[arguments]: Likewise.
* gnu/packages/image-processing.scm (opencv, itk-snap)[arguments]: Likewise.
* gnu/packages/image.scm (freeimage)[arguments]: Likewise.
* gnu/packages/kodi.scm (crossguid)[arguments]: Likewise.
* gnu/packages/music.scm (amsynth, qmidiarp, qmidiroute, seq24)[arguments]: Likewise.
* gnu/packages/pdf.scm (python-poppler-qt5)[arguments]: Likewise.
* gnu/packages/sagemath.scm (lcalc)[arguments]: Likewise.
* gnu/packages/video.scm (vlc, mlt, v4l-utils)[arguments]: Likewise.
 2019-10-20 14:00:12 +02:00
Ricardo Wurmus
b847b06dc3
gnu: r-rhdf5lib: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
ddebbee6d7
gnu: r-hdf5array: Update to 1.12.3. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
a15c68bfac
gnu: r-gwascat: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
5d23d9b1c5
gnu: r-ldblock: Update to 1.14.3. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
86d5ab8bf4
gnu: r-ensembldb: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
f0f73313e3
gnu: r-keggrest: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
8c65e219f7
gnu: r-rhdf5: Update to 2.28.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1.
 2019-10-18 20:35:27 +02:00
Ricardo Wurmus
be0af9cc8b
gnu: r-rhtslib: Update to 1.16.3. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3.
 2019-10-18 20:35:26 +02:00
Ricardo Wurmus
b62780d9f9
gnu: r-rsamtools: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3.
 2019-10-18 20:35:26 +02:00
Ricardo Wurmus
195b18b58e
gnu: bowtie1: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3.
 2019-10-18 20:35:26 +02:00
Marius Bakke
b95d1b3289
Merge branch 'master' into staging 2019-10-18 18:10:47 +02:00
Ricardo Wurmus
19e4261837
gnu: Add methyldackel. 
* gnu/packages/bioinformatics.scm (methyldackel): New variable.
 2019-10-14 22:49:04 +02:00
Ricardo Wurmus
b06cdce923
gnu: Add r-velocyto. 
* gnu/packages/bioinformatics.scm (r-velocyto): New variable.
 2019-10-14 18:22:46 +02:00
Julien Lepiller
2b8491fbbe
gnu: mariadb: Split into out, lib and dev. 
* gnu/packages/databases.scm (mariadb): Split into out, lib and dev.
(perl-dbd-mysql, python-mysqlclient): Adjust dependencies.
* gnu/packages/bioinformatics.scm (kentutils): Adjust dependencies.
* gnu/packages/cran.scm (r-rmysql): Adjust dependencies.
* gnu/packages/emacs-xyz.scm (emacs-emacsql): Adjust dependencies.
* gnu/packages/kodi.scm (kodi): Adjust dependencies.
* gnu/packages/qt.scm (qt, qtbase): Adjust dependencies.
* gnu/packages/ruby.scm (ruby-mysql2): Adjust dependencies.
 2019-10-12 13:07:41 +02:00
Ludovic Courtès
4d8d2fbaf3
Merge branch 'master' into core-updates 2019-10-07 17:06:13 +02:00
Ricardo Wurmus
33651044c6
gnu: r-seurat: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1.
[propagated-inputs]: Add r-httr.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus
94638cbe77
gnu: r-rsamtools: Update to 2.0.2. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
 2019-10-06 23:08:47 +02:00
Ricardo Wurmus
122c1b3ce7
gnu: r-biomart: Update to 2.40.5. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
 2019-10-06 23:08:46 +02:00
Ricardo Wurmus
e08902d3cb
Merge branch 'master' into core-updates 2019-10-06 22:02:20 +02:00
Tobias Geerinckx-Rice
5767547e73
gnu: rcas-web: Fix build with RCAS > 1.3.x. 
* gnu/packages/bioinformatics.scm (rcas-web)[arguments]: Add ‘find-RCAS’ phase.
 2019-10-03 16:03:36 +02:00
Ludovic Courtès
0cf2b6f2db
Merge branch 'master' into core-updates 2019-10-01 12:06:00 +02:00
Ricardo Wurmus
e0c6c18371
gnu: r-gviz: Update to 1.28.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.3.
 2019-09-28 12:24:15 +02:00
Ricardo Wurmus
b0a5be065e
gnu: r-mzr: Update to 2.18.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.1.
 2019-09-28 12:24:15 +02:00
Ricardo Wurmus
80004ec013
gnu: r-rhtslib: Update to 1.16.2. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.2.
 2019-09-28 12:24:15 +02:00
Ricardo Wurmus
272cb5a23f
gnu: r-rsamtools: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.1.
 2019-09-28 12:24:15 +02:00
Ricardo Wurmus
d0983f294b
gnu: r-iranges: Update to 2.18.3. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.3.
 2019-09-28 12:24:15 +02:00
Ludovic Courtès
9ff87bb996
Merge branch 'master' into core-updates 2019-09-17 16:27:15 +02:00
Ricardo Wurmus
9eac315069
gnu: r-delayedmatrixstats: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
 2019-09-14 23:39:39 +02:00
Ricardo Wurmus
82e343d14a
gnu: r-rhdf5lib: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
 2019-09-14 23:39:25 +02:00
Ricardo Wurmus
cd25e29616
gnu: r-rtracklayer: Update to 1.44.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
 2019-09-14 23:39:20 +02:00
Ricardo Wurmus
146f0ba5d1
gnu: r-genomicranges: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
 2019-09-14 23:39:12 +02:00
Ricardo Wurmus
7f518ef70b
gnu: r-s4vectors: Update to 0.22.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
 2019-09-14 23:39:08 +02:00