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2215 commits

Author SHA1 Message Date
Tobias Geerinckx-Rice
030fe2fb7e
gnu: miso: Update home page. 
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
b725655fce
gnu: grit: Update home page. 
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
b56f2b6366
gnu: express-beta-diversity: Update home page. 
The original is not coming back:
<https://github.com/dparks1134/ExpressBetaDiversity/issues/11>.

* gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]:
Use source code repository as home page.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
568bd2e382
gnu: dendropy: Update home page. 
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
99db6db7be
gnu: Use HTTPS for bioconductor.org. 
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
* gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
 2020-01-21 00:43:39 +01:00
Tobias Geerinckx-Rice
f1fa954a7d
gnu: edirect: Use HTTPS home page. 
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
 2020-01-19 06:09:02 +01:00
Marius Bakke
7699e32289
gnu: kentutils: Build with OpenSSL 1.0. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
 2020-01-16 19:20:20 +01:00
Ricardo Wurmus
d64124df89
gnu: r-delayedarray: Update to 0.12.2. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
 2020-01-16 06:53:31 +01:00
Ricardo Wurmus
f7b5c1a02f
gnu: r-iranges: Update to 2.20.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
 2020-01-16 06:53:31 +01:00
Ricardo Wurmus
fdf69f1ee0
gnu: r-s4vectors: Update to 0.24.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
 2020-01-16 06:53:31 +01:00
Ricardo Wurmus
7241b44ad4
gnu: r-biocstyle: Update to 2.14.4. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
 2020-01-16 06:53:30 +01:00
Efraim Flashner
2604ecb3a9
gnu: smithwaterman: Update to 0.0.0-2.2610e25. 
* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25.
[arguments]: Add make-flags to build static library. Adjust custom
'install phase to install static library.
 2020-01-09 14:30:38 +02:00
Efraim Flashner
0ab7f6c5f4
gnu: vcflib: Update to 1.0.1. 
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1.
[source]: Download using url-fetch.
[native-inputs]: Sort alphabetically. Move perl, python ...
[inputs]: ... to here.
[arguments]: Add make-flags. Update custom 'build phase.

(tabixpp-freebayes): Remove variable.
(freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes.
 2020-01-09 14:30:38 +02:00
Efraim Flashner
2e3efa6e55
gnu: fastahack: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
 2020-01-09 14:30:38 +02:00
Efraim Flashner
de933b71ee
gnu: Add intervaltree. 
* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
 2020-01-09 14:30:38 +02:00
Efraim Flashner
612d6a8e5b
gnu: tabixpp: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.0.
[source]: Add snippet to remove vendored library.
[arguments]: Adjust custom 'build phase to fix INCLUDES.
 2020-01-09 14:30:37 +02:00
Efraim Flashner
2673620f24
gnu: bwa: Install static library. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
 2020-01-09 14:30:34 +02:00
Pierre Neidhardt
ba42da245b
gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition. 
This fixes the bug which prevented uglify-js from being defined properly, and
cascaded back to all Common Lisp packages.

* gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz.
* gnu/packages/cran.scm: Use lisp-xyz module.
* gnu/packages/javascript.scm (uglify-js): Move from here...
* gnu/packages/lisp-xyz.scm: ... To here.
* gnu/packages/web.scm: Replace javascript module with lisp-xyz.
* guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module.
 2020-01-03 15:03:36 +01:00
Ricardo Wurmus
04b181cb15
gnu: r-topgo: Update to 2.38.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
 2019-12-27 21:30:25 +01:00
Ricardo Wurmus
4997ff5c1b
gnu: r-summarizedexperiment: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
 2019-12-27 21:30:25 +01:00
Ricardo Wurmus
ba17429d67
gnu: r-delayedarray: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
 2019-12-27 21:30:25 +01:00
Ricardo Wurmus
152a408051
gnu: r-biocparallel: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
 2019-12-27 21:30:25 +01:00
Ricardo Wurmus
827d0fa846
gnu: r-shortread: Update to 1.44.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
 2019-12-27 21:30:21 +01:00
Brett Gilio
5bc95d2bcd
gnu: python-bbknn: Update to 1.3.6. 
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.3.6.
[arguments]: Disable tests until migration to python-scikit-learn.
[propgated-inputs]: Remove python-faiss, python-scanpy.
[propgated-inputs]: Add python-scipy, python-umap-learn.
 2019-12-23 17:31:06 -06:00
Mădălin Ionel Patrașcu
3bedd9f40f
gnu: tophat: Build with GCC 5 
* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
(tophat)[inputs]: Reorder alphabetically the dependencies.
(tophat)[home-page]: Swapp to https.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-12-23 19:38:14 +01:00
Mădălin Ionel Patrașcu
345488d76f
gnu: fastx-toolkit: Build with GCC 6 
* gnu/packages/bioinformatics.scm (fastx-toolkit)[native-inputs]: Add gcc-6.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-12-21 23:55:25 +01:00
Ricardo Wurmus
61e21c0899
gnu: r-scater: Update to 1.14.6. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
 2019-12-20 21:26:26 +01:00
Ricardo Wurmus
595036d9f9
gnu: Add libsbml. 
* gnu/packages/bioinformatics.scm (libsbml): New variable.
 2019-12-17 20:02:11 +01:00
Ricardo Wurmus
f98480a975
gnu: r-seurat: Update to 3.1.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
94f9c0cdc4
gnu: python-gffutils: Update description. 
* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.
 2019-12-16 23:32:55 +01:00
Mădălin Ionel Patrașcu
cfd83f3282
gnu: Add python-gffutils. 
* gnu/packages/bioinformatics.scm (python-gffutils): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-16 23:27:00 +01:00
Mădălin Ionel Patrașcu
4ade2dd9d2
gnu: python-pyfaidx: Update to 0.5.7. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
 2019-12-16 23:22:12 +01:00
Ricardo Wurmus
0726645eca
gnu: r-genefilter: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0.
[propagated-inputs]: Remove r-s4vectors and add r-biocgenerics.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
867018e138
gnu: r-deseq2: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
ebc81e300c
gnu: r-dexseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
12c4555d44
gnu: r-annotationforge: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
33a2acb757
gnu: r-rbgl: Update to 1.62.1. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
d2661841be
gnu: r-gseabase: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
4afcf941d2
gnu: r-category: Update to 2.52.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
545730891e
gnu: r-gostats: Update to 2.52.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
f29c9f0d33
gnu: r-shortread: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus
58fd68b299
gnu: r-systempiper: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
f8f815667d
gnu: r-grohmm: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.20.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
74d59b6748
gnu: r-biocviews: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
ef96154433
gnu: r-biocstyle: Update to 2.14.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
7758d5205c
gnu: r-bioccheck: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.22.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
d37daf8929
gnu: r-s4vectors: Update to 0.24.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.1.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
d2723484f6
gnu: r-iranges: Update to 2.20.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.1.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
937f3a46eb
gnu: r-genomeinfodb: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus
da03fa3c90
gnu: r-edger: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.0.
 2019-12-15 15:39:03 +01:00