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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
19e4261837
gnu: Add methyldackel.
...
* gnu/packages/bioinformatics.scm (methyldackel): New variable.
2019-10-14 22:49:04 +02:00
b06cdce923
gnu: Add r-velocyto.
...
* gnu/packages/bioinformatics.scm (r-velocyto): New variable.
2019-10-14 18:22:46 +02:00
4d8d2fbaf3
Merge branch 'master' into core-updates
2019-10-07 17:06:13 +02:00
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
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
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
e08902d3cb
Merge branch 'master' into core-updates
2019-10-06 22:02:20 +02:00
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
0cf2b6f2db
Merge branch 'master' into core-updates
2019-10-01 12:06:00 +02:00
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
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
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
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
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
9ff87bb996
Merge branch 'master' into core-updates
2019-09-17 16:27:15 +02:00
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
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
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
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
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
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
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
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
65542a8852
Merge branch 'master' into core-updates
2019-09-06 20:46:00 -04:00
8205534569
gnu: Add samblaster.
...
* gnu/packages/bioinformatics.scm (samblaster): New variable.
2019-09-06 15:00:49 +02:00
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
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
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
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
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
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
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
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
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
Efraim Flashner
Timothy Sample
Ricardo Wurmus
Marius Bakke
Ludovic Courtès
Tobias Geerinckx-Rice
Mark H Weaver
Christopher Baines