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2148 Commits

Author SHA1 Message Date
Ricardo Wurmus
43058ca656
gnu: r-chipseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.36.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus
746e1f062e
gnu: r-copywriter: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.18.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus
32f6059635
gnu: r-affy: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.64.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus
51ca216bdf
gnu: r-affyio: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus
065c305ca5
gnu: r-methylkit: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus
2a6ce98b17
gnu: r-sva: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus
d12328f9fe
gnu: r-protgenerics: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.18.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus
3381dc4b5c
gnu: r-mzr: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0.
 2019-12-15 15:38:56 +01:00
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
Ricardo Wurmus
d40ebbf228
gnu: r-gprofiler: Update to 0.6.8. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus
8e70b33c56
gnu: r-annotationhub: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus
f70599cb78
gnu: r-edger: Update to 3.26.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
 2019-09-08 00:30:33 +02:00
Mark H Weaver
65542a8852
Merge branch 'master' into core-updates 2019-09-06 20:46:00 -04:00
Ricardo Wurmus
8205534569
gnu: Add samblaster. 
* gnu/packages/bioinformatics.scm (samblaster): New variable.
 2019-09-06 15:00:49 +02:00
Ricardo Wurmus
f480133c4e
gnu: libbigwig: Update to 0.4.4. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
 2019-09-05 22:45:41 +02:00
Christopher Baines
067ea2989f
gnu: python-pyfaidx: Remove python-setuptools as an input. 
As this is provided by the build system, and I'm assuming that it's not
necessary to have it as a propagated input.

* gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove
python-setuptools.
 2019-09-05 18:35:47 +02:00
Christopher Baines
5f9fe21d49
gnu: umi-tools: Remove python-setuptools as an input. 
As this is provided by the build system.

* gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove
python-setuptools.
 2019-09-05 18:35:42 +02:00
Ricardo Wurmus
79c6d8781b
gnu: bwa-meth: Capture one more reference to "bwa". 
Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of
"bwa index" to retain reference to "bwa" package.
 2019-09-05 12:06:43 +02:00
Ricardo Wurmus
e107ccea84
gnu: r-ldblock: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2.
[propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and
r-httr.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus
32fcd898f0
gnu: r-seurat: Update to 3.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0.
[propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus
91addfe05c
gnu: r-rtracklayer: Update to 1.44.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus
2c7a32c2ac
gnu: r-biomart: Update to 2.40.4. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus
e5bc6fce19
gnu: r-annotationdbi: Update to 1.46.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus
aea33b475b
gnu: r-iranges: Update to 2.18.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2.
 2019-09-02 14:40:56 +02:00
Robert Vollmert
dddbc90c64
gnu: Move non-compilers out of haskell.scm. 
* gnu/packages/haskell.scm (ghc-abstract-deque, ghc-abstract-par,
ghc-adjunctions, ghc-aeson-compat, ghc-alex, ghc-alsa-core,
ghc-annotated-wl-pprint, ghc-ansi-terminal, ghc-ansi-wl-pprint,
ghc-appar, ghc-async, ghc-atomic-write, ghc-attoparsec,
ghc-attoparsec-bootstrap, ghc-attoparsec-iso8601, ghc-auto-update,
ghc-aws, ghc-base16-bytestring, ghc-base64-bytestring, ghc-base-compat,
ghc-basement, ghc-base-orphans, ghc-base-prelude,
ghc-base-unicode-symbols, ghc-bifunctors, ghc-bindings-dsl,
ghc-blaze-builder, ghc-blaze-markup, ghc-bloomfilter, ghc-boxes,
ghc-byteable, ghc-byteorder, ghc-bytes, ghc-bytestring-builder,
ghc-bytestring-handle, ghc-bytestring-lexing, ghc-bzlib-conduit,
ghc-c2hs, ghc-cairo, ghc-call-stack, ghc-call-stack-boot,
ghc-case-insensitive, ghc-cereal, ghc-cereal-conduit, ghc-cgi,
ghc-charset, ghc-chart, ghc-chart-cairo, ghc-chasingbottoms,
ghc-cheapskate, ghc-chell, ghc-chell-quickcheck, ghc-chunked-data,
ghc-clock, ghc-clock-bootstrap, ghc-cmark, ghc-cmark-gfm, ghc-cmdargs,
ghc-code-page, ghc-colour, ghc-comonad, ghc-concatenative,
ghc-concurrent-output, ghc-conduit, ghc-conduit-algorithms,
ghc-conduit-combinators, ghc-conduit-extra, ghc-configurator,
ghc-connection, ghc-constraints, ghc-contravariant,
ghc-contravariant-extras, ghc-convertible, ghc-data-accessor,
ghc-data-accessor-transformers, ghc-data-default,
ghc-data-default-class, ghc-data-default-instances-base,
ghc-data-default-instances-containers, ghc-data-default-instances-dlist,
ghc-data-default-instances-old-locale, ghc-data-hash, ghc-data-ordlist,
ghc-deepseq-generics, ghc-descriptive, ghc-diff, ghc-disk-free-space,
ghc-distributive, ghc-dlist, ghc-doctemplates, ghc-doctest,
ghc-double-conversion, ghc-easy-file, ghc-easyplot, ghc-echo,
ghc-edisonapi, ghc-edisoncore, ghc-edit-distance, ghc-either,
ghc-email-validate, ghc-enclosed-exceptions, ghc-equivalence, ghc-erf,
ghc-errorcall-eq-instance, ghc-errors, ghc-esqueleto, ghc-exactprint,
ghc-exceptions, ghc-executable-path, ghc-extensible-exceptions,
ghc-extra, ghc-fail, ghc-fast-logger, ghc-feed, ghc-fgl,
ghc-fgl-arbitrary, ghc-file-embed, ghc-filemanip, ghc-findbin,
ghc-fingertree, ghc-fixed, ghc-foldl, ghc-foundation, ghc-free,
ghc-fsnotify, ghc-generic-deriving, ghc-generics-sop,
ghc-geniplate-mirror, ghc-genvalidity, ghc-genvalidity-property,
ghc-gitrev, ghc-glob, ghc-gluraw, ghc-glut, ghc-gnuplot, ghc-graphviz,
ghc-gtk2hs-buildtools, ghc-hackage-security, ghc-haddock,
ghc-haddock-api, ghc-haddock-library, ghc-half, ghc-happy, ghc-hashable,
ghc-hashable-bootstrap, ghc-hashable-time, ghc-hashtables,
ghc-haskell-lexer, ghc-haskell-src, ghc-haskell-src-exts,
ghc-haskell-src-exts-util, ghc-haskell-src-meta, ghc-hasktags, ghc-hex,
ghc-highlighting-kate, ghc-hindent, ghc-hinotify, ghc-hmatrix,
ghc-hmatrix-gsl, ghc-hmatrix-gsl-stats, ghc-hmatrix-special,
ghc-hostname, ghc-hourglass, ghc-hpack, ghc-hs-bibutils, ghc-hslogger,
ghc-hslua, ghc-hslua-module-text, ghc-http-api-data, ghc-ieee754,
ghc-ifelse, ghc-indents, ghc-inline-c, ghc-inline-c-cpp,
ghc-integer-logarithms, ghc-integer-logarithms-bootstrap,
ghc-interpolate, ghc-intervalmap, ghc-invariant, ghc-iproute, ghc-iwlib,
ghc-json, ghc-juicypixels, ghc-kan-extensions, ghc-language-c,
ghc-language-haskell-extract, ghc-lens, ghc-libffi, ghc-libmpd,
ghc-libxml, ghc-lifted-async, ghc-lifted-base, ghc-linear,
ghc-logging-facade, ghc-logict, ghc-lzma, ghc-lzma-conduit,
ghc-markdown-unlit, ghc-math-functions, ghc-megaparsec, ghc-memory,
ghc-memotrie, ghc-microlens, ghc-microlens-ghc, ghc-microlens-mtl,
ghc-microlens-platform, ghc-microlens-th, ghc-missingh, ghc-mmap,
ghc-mmorph, ghc-mockery, ghc-monad-control, ghc-monad-logger,
ghc-monad-loops, ghc-monad-par, ghc-monad-par-extras, ghc-monadplus,
ghc-monadrandom, ghc-monads-tf, ghc-mono-traversable, ghc-murmur-hash,
ghc-mwc-random, ghc-nats, ghc-nats-bootstrap, ghc-network,
ghc-network-info, ghc-network-uri, ghc-newtype-generics, ghc-objectname,
ghc-old-locale, ghc-old-time, ghc-opengl, ghc-openglraw,
ghc-operational, ghc-options, ghc-optparse-applicative, ghc-pandoc,
ghc-pandoc-citeproc, ghc-pandoc-types, ghc-parallel, ghc-parsec-numbers,
ghc-parser-combinators, ghc-parsers, ghc-path, ghc-path-io, ghc-paths,
ghc-patience, ghc-pcre-light, ghc-persistent, ghc-persistent-sqlite,
ghc-persistent-template, ghc-polyparse, ghc-pqueue, ghc-prelude-extras,
ghc-pretty-hex, ghc-pretty-show, ghc-primitive, ghc-profunctors,
ghc-psqueues, ghc-random, ghc-raw-strings-qq, ghc-rebase, ghc-reducers,
ghc-refact, ghc-reflection, ghc-regex, ghc-regex-applicative,
ghc-regex-base, ghc-regex-compat, ghc-regex-compat-tdfa,
ghc-regex-pcre-builtin, ghc-regex-posix, ghc-regex-tdfa,
ghc-regex-tdfa-text, ghc-rerebase, ghc-resolv, ghc-resource-pool,
ghc-resourcet, ghc-rfc5051, ghc-rio, ghc-safe, ghc-safe-exceptions,
ghc-safeio, ghc-safesemaphore, ghc-sandi, ghc-scientific,
ghc-scientific-bootstrap, ghc-sdl, ghc-sdl-image, ghc-sdl-mixer,
ghc-securemem, ghc-semigroupoids, ghc-semigroups,
ghc-semigroups-bootstrap, ghc-setenv, ghc-setlocale, ghc-shakespeare,
ghc-shelly, ghc-silently, ghc-simple-reflect, ghc-simple-sendfile,
ghc-skylighting-core, ghc-skylighting, ghc-smallcheck, ghc-socks,
ghc-split, ghc-statevar, ghc-statistics, ghc-stm-chans, ghc-stm-conduit,
ghc-stmonadtrans, ghc-storable-complex, ghc-streaming-commons,
ghc-strict, ghc-stringbuilder, ghc-string-qq, ghc-stringsearch,
ghc-stylish-haskell, ghc-syb, ghc-system-fileio, ghc-system-filepath,
ghc-tagged, ghc-tar, ghc-temporary, ghc-temporary-rc, ghc-terminal-size,
ghc-texmath, ghc-text-binary, ghc-tf-random, ghc-th-abstraction,
ghc-th-expand-syns, ghc-th-lift, ghc-th-lift-instances, ghc-th-orphans,
ghc-th-reify-many, ghc-time-locale-compat, ghc-tldr,
ghc-transformers-base, ghc-transformers-compat, ghc-tree-diff,
ghc-trifecta, ghc-tuple-th, ghc-typed-process, ghc-unbounded-delays,
ghc-unexceptionalio, ghc-union-find, ghc-uniplate, ghc-unix-compat,
ghc-unix-time, ghc-unliftio, ghc-unliftio-core,
ghc-unordered-containers, ghc-unordered-containers-bootstrap,
ghc-uri-bytestring, ghc-utf8-string, ghc-utility-ht, ghc-uuid,
ghc-uuid-types, ghc-validation, ghc-validity, ghc-vault, ghc-vector,
ghc-vector-algorithms, ghc-vector-binary-instances, ghc-vector-builder,
ghc-vector-th-unbox, ghc-void, ghc-wave, ghc-wcwidth,
ghc-wcwidth-bootstrap, ghc-weigh, ghc-wl-pprint,
ghc-wl-pprint-annotated, ghc-wl-pprint-text, ghc-word8, ghc-x11,
ghc-x11-xft, ghc-xdg-basedir, ghc-xml, ghc-xml-conduit, ghc-xml-types,
ghc-yaml, ghc-zip-archive, ghc-zlib): Move variables from here...
* gnu/packages/haskell-xyz.scm: ...to here.
* gnu/packages/agda.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/cran.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/games.scm,
gnu/packages/graphics.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-check.scm,
gnu/packages/idris.scm,
gnu/packages/statistics.scm,
gnu/packages/wm.scm: Update module references.

Co-authored-by: Timothy Sample <samplet@ngyro.com>
 2019-08-31 09:25:49 -04:00
Mark H Weaver
893c2df00d
Merge branch 'master' into core-updates 2019-08-22 15:53:27 -04:00
Efraim Flashner
d371112bd0
gnu: edirect: Update to 12.1.20190819. 
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819.
 2019-08-20 11:08:42 +03:00
Ricardo Wurmus
a6a19fb14c
gnu: r-gviz: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1.
 2019-08-19 16:25:33 +02:00
Ricardo Wurmus
b65bd33c36
gnu: r-edger: Update to 3.26.7. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.7.
 2019-08-16 22:41:27 +02:00
Marius Bakke
462ad9f56b
Merge branch 'master' into core-updates 2019-08-13 20:42:06 +02:00
Ricardo Wurmus
c2847323d8
gnu: freebayes: Simplify and enable tests. 
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set
make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles"
phase; move build of tabixpp and vcflib to separate phase
"build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build"
phase.
 2019-08-09 12:15:26 +02:00
Ricardo Wurmus
7cd98e868e
gnu: freebayes: Move bamtools to inputs. 
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools
from here...
[inputs]: ...to here.
 2019-08-09 12:15:26 +02:00
Pierre Neidhardt
8803dbdad8
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-09 10:47:25 +03:00
Pierre Neidhardt
95fb1a1851
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
(tabixpp-freebayes): New private variable.
 2019-08-09 10:43:40 +03:00
Ricardo Wurmus
90060e2071
gnu: r-hdf5array: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus
a39f2e4cea
gnu: r-biocparallel: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
 2019-08-08 16:47:02 +02:00
Efraim Flashner
1a069a170c
Revert "gnu: Add vcflib." 
This reverts commit 194e45f90a.

This commit does not have a good commit message, and it breaks master
 2019-08-08 15:34:05 +03:00
Efraim Flashner
6bc63fd8a7
Revert "gnu: Add freebayes." 
This reverts commit 173e046950.
 2019-08-08 15:32:51 +03:00
Pierre Neidhardt
173e046950
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-08 15:18:34 +03:00
Pierre Neidhardt
194e45f90a
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
 2019-08-08 15:18:33 +03:00
Pierre Neidhardt
7d71557d4d
gnu: Add fastahack. 
* gnu/packages/bioinformatics.scm (fastahack): New variable.
 2019-08-08 15:18:32 +03:00
Pierre Neidhardt
70782dddff
gnu: Add fsom. 
* gnu/packages/bioinformatics.scm (fsom): New variable.
 2019-08-08 15:18:31 +03:00
Pierre Neidhardt
8cd51276e5
gnu: Add multichoose. 
* gnu/packages/bioinformatics.scm (multichoose): New variable.
 2019-08-08 15:18:30 +03:00
Pierre Neidhardt
7faa70cf2b
gnu: Add smithwaterman. 
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
 2019-08-08 15:18:29 +03:00
Pierre Neidhardt
62a031afc4
gnu: Add tabixpp. 
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
 2019-08-08 15:18:14 +03:00
Robert Vollmert
a1eb8be8ca
gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml. 
These are ghc-8.4-bundled packages, removing to avoid build
conflicts.

* gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove.
* gnu/packages/haskell-web.scm (ghc-xhtml): Remove.
* gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text.
* gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and
ghc-text.
* gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec.
(git-annex)[inputs]: Remove ghc-stm and ghc-text.
(ghc-sdl2)[inputs]: Remove ghc-text.
(ghc-sdl2-image)[inputs]: Remove ghc-text.
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm.
(ghc-tasty)[inputs]: Remove ghc-stm.
(ghc-tasty-rerun)[inputs]: Same.
(ghc-quickcheck-instances)[inputs]: Remove ghc-text.
(ghc-hedgehog)[inputs]: Remove ghc-stm.
* gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove
ghc-text.
* gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text.
(ghc-cookie)[inputs]: Same.
(ghc-http-types)[inputs]: Same.
(ghc-http)[inputs]: Remove ghc-parsec.
(ghc-http-client)[inputs]: Remove ghc-text.
(ghc-http2)[inputs]: Remove ghc-stm.
(ghc-http-conduit)[native-inputs]: Remove ghc-text.
(ghc-wai)[inputs]: Same.
(ghc-wai-extra)[inputs]: Same.
(ghc-warp)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xss-sanitize)[native-inputs]: Remove ghc-text.
(ghc-css-text)[inputs]: Same.
(ghc-mime-types)[inputs]: Same.
(ghc-blaze-html)[inputs]: Same.
(ghc-aeson)[inputs]: Same.
(ghc-aeson-pretty)[inputs]: Same.
(ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-multipart)[inputs]: Remove ghc-parsec.
(ghc-uri-encode)[inputs]: Remove ghc-text.
(ghc-path-pieces)[inputs]: Same.
(ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-yesod-persistent)[inputs]: Remove ghc-text.
(ghc-yesod-form)[inputs]: Same.
(ghc-yesod)[inputs]: Same.
(ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-hxt)[inputs]: Remove ghc-parsec.
* gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text.
(ghc-double-conversion)[inputs]: Same.
(ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text.
[native-inputs]: Remove ghc-parsec.
(ghc-cgi)[inputs]: Remove ghc-parsec.
(hlint)[inputs]: Remove ghc-text.
(ghc-openglraw)[inputs]: Remove ghc-text.
(ghc-opengl)[inputs]: Same.
(ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text.
(ghc-hackage-security)[inputs]: Remove ghc-parsec.
(cabal-install)[inputs]: Remove ghc-stm.
(ghc-parsec-numbers)[inputs]: Remove ghc-parsec.
(ghc-safesemaphore)[inputs]: Remove ghc-stm.
(ghc-text-binary)[inputs]: Remove ghc-text.
(ghc-hashable)[inputs]: Remove ghc-text.
(ghc-transformers-base)[inputs]: Remove ghc-stm.
(ghc-indents)[inputs]: Remove ghc-parsec.
(ghc-regex-tdfa-rc)[inputs]: Same.
(ghc-regex-tdfa-text)[inputs]: Same.
(ghc-regex)[inputs]: Remove ghc-text.
(ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-attoparsec)[inputs]: Remove ghc-text.
(ghc-attoparsec-bootstrap)[inputs]: Same.
(ghc-zip-archive)[inputs]: Same.
(ghc-polyparse)[inputs]: Same.
(ghc-reducers)[inputs]: Same.
(ghc-xml)[inputs]: Same.
(ghc-feed)[inputs]: Same.
(ghc-exceptions)[inputs]: Remove ghc-stm.
(ghc-case-insensitive)[inputs]: Remove ghc-text.
(ghc-megaparsec)[inputs]: Same.
(ghc-network-uri)[inputs]: Remove ghc-parsec.
(ghc-monad-control)[inputs]: Remove ghc-stm.
(ghc-blaze-builder)[inputs]: Remove ghc-text.
(ghc-blaze-markup)[inputs]: Same.
(ghc-async)[inputs]: Remove ghc-stm.
(ghc-invariant)[inputs]: Same.
(ghc-statevar)[inputs]: Same.
(ghc-lens)[inputs]: Remove ghc-text.
(ghc-cheapskate)[inputs]: Same.
(ghc-semigroups)[inputs]: Same.
(ghc-semigroups-bootstrap)[inputs]: Same.
(ghc-fast-logger)[inputs]: Same.
(ghc-scientific)[inputs]: Same.
(ghc-scientific-bootstrap)[inputs]: Same.
(ghc-texmath)[inputs]: Remove ghc-parsec.
(ghc-highlighting-kate)[inputs]: Same.
(ghc-cmark)[inputs]: Remove ghc-text.
(ghc-cmark-gfm)[inputs]: Same.
(ghc-th-lift-instances)[inputs]: Same.
(ghc-yaml)[inputs]: Same.
(ghc-hslua)[inputs]: Same.
(ghc-hslua-module-text)[inputs]: Same.
(ghc-skylighting-core)[inputs]: Same.
(ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-pandoc)[inputs]: Same.
(ghc-typed-process)[inputs]: Remove ghc-stm.
(ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xml-types)[inputs]: Remove ghc-text.
(ghc-xml-conduit)[inputs]: Same.
(ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-regex-tdfa)[inputs]: Remove ghc-parsec.
(ghc-wl-pprint-text)[inputs]: Remove ghc-text.
(ghc-graphviz)[inputs]: Same.
(ghc-system-filepath-bootstrap)[inputs]: Same.
(ghc-system-fileio-bootstrap)[inputs]: Same.
(ghc-shelly)[inputs]: Same.
(ghc-chell)[inputs]: Same.
(ghc-system-filepath)[inputs]: Same.
(ghc-system-fileio)[inputs]: Same.
(ghc-fsnotify)[inputs]: Same.
(ghc-json)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-esqueleto)[inputs]: Remove ghc-text.
(shellcheck)[inputs]: Remove ghc-parsec.
(ghc-errors)[inputs]: Remove ghc-text.
(ghc-chunked-data)[inputs]: Same.
(ghc-uuid-types)[inputs]: Same.
(ghc-uuid)[inputs]: Same.
(ghc-rebase)[inputs]: Remove ghc-stm and ghc-text.
(ghc-foldl)[inputs]: Remove ghc-text.
(ghc-mono-traversable)[inputs]: Same.
(ghc-conduit-combinators)[inputs]: Same.
(ghc-aws)[inputs]: Same.
(ghc-stm-chans)[inputs]: Remove ghc-stm.
(ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm.
(ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-resource-pool)[inputs]: Remove ghc-stm.
(ghc-attoparsec-iso8601)[inputs]: Remove ghc-text.
(ghc-http-api-data)[inputs]: Same.
(ghc-persistent)[inputs]: Same.
(ghc-aeson-compat)[inputs]: Same.
(ghc-persistent-template)[inputs]: Same.
(ghc-unliftio)[inputs]: Remove ghc-stm.
(ghc-persistent-sqlite)[native-inputs]: Remove ghc-text.
(ghc-bytes)[inputs]: Same.
(ghc-missingh)[inputs]: Remove ghc-parsec.
(ghc-rio)[inputs]: Remove ghc-text.
(ghc-cairo)[inputs]: Same.
(ghc-atomic-write)[inputs]: Remove ghc-text.
[native-inputs]: Same.
(ghc-stm-conduit)[inputs]: Remove ghc-stm.
(ghc-conduit-algorithms)[inputs]: Same.
(ghc-interpolate)[native-inputs]: Remove ghc-text.
(ghc-hpack)[inputs]: Same.
(ghc-inline-c)[inputs]: Remove ghc-parsec.
(ghc-configurator)[inputs]: Remove ghc-text.
(ghc-c2hs)[native-inputs]: Same.
(ghc-libmpd)[inputs]: Same.
(ghc-concurrent-output)[inputs]: Remove ghc-stm.
* gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text.
* gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-08-07 22:05:29 -04:00
Ricardo Wurmus
c8e141ab02
gnu: r-msnid: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus
afe4be49f1
gnu: r-rcas: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus
76d9b08e1b
gnu: r-genomicfeatures: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
e16fe0b50a
gnu: r-rtracklayer: Update to 1.44.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
6f8760d9f8
gnu: r-summarizedexperiment: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
 2019-08-06 15:48:59 +02:00