f1fa954a7d
gnu: edirect: Use HTTPS home page.
...
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
2020-01-19 06:09:02 +01:00
7699e32289
gnu: kentutils: Build with OpenSSL 1.0.
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* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
2020-01-16 19:20:20 +01:00
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
f7b5c1a02f
gnu: r-iranges: Update to 2.20.2.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
2020-01-16 06:53:31 +01:00
fdf69f1ee0
gnu: r-s4vectors: Update to 0.24.2.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
2020-01-16 06:53:31 +01:00
7241b44ad4
gnu: r-biocstyle: Update to 2.14.4.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
2020-01-16 06:53:30 +01:00
2604ecb3a9
gnu: smithwaterman: Update to 0.0.0-2.2610e25.
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* 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
0ab7f6c5f4
gnu: vcflib: Update to 1.0.1.
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* 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
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
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
612d6a8e5b
gnu: tabixpp: Update to 1.1.0.
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* 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
2673620f24
gnu: bwa: Install static library.
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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
2020-01-09 14:30:34 +02:00
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
04b181cb15
gnu: r-topgo: Update to 2.38.1.
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* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27 21:30:25 +01:00
4997ff5c1b
gnu: r-summarizedexperiment: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27 21:30:25 +01:00
ba17429d67
gnu: r-delayedarray: Update to 0.12.1.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27 21:30:25 +01:00
152a408051
gnu: r-biocparallel: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27 21:30:25 +01:00
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
5bc95d2bcd
gnu: python-bbknn: Update to 1.3.6.
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* 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
3bedd9f40f
gnu: tophat: Build with GCC 5
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* 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
345488d76f
gnu: fastx-toolkit: Build with GCC 6
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* 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
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
595036d9f9
gnu: Add libsbml.
...
* gnu/packages/bioinformatics.scm (libsbml): New variable.
2019-12-17 20:02:11 +01:00
f98480a975
gnu: r-seurat: Update to 3.1.2.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
2019-12-17 14:58:32 +01:00
94f9c0cdc4
gnu: python-gffutils: Update description.
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* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.
2019-12-16 23:32:55 +01:00
cfd83f3282
gnu: Add python-gffutils.
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* gnu/packages/bioinformatics.scm (python-gffutils): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2019-12-16 23:27:00 +01:00
4ade2dd9d2
gnu: python-pyfaidx: Update to 0.5.7.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
2019-12-16 23:22:12 +01:00
0726645eca
gnu: r-genefilter: Update to 1.68.0.
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* 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
867018e138
gnu: r-deseq2: Update to 1.26.0.
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* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
2019-12-15 15:39:04 +01:00
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
12c4555d44
gnu: r-annotationforge: Update to 1.28.0.
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* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
2019-12-15 15:39:04 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
8f5d2c3abc
gnu: r-variantannotation: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.32.0.
2019-12-15 15:39:03 +01:00
eea491e5c6
gnu: r-limma: Update to 3.42.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.0.
2019-12-15 15:39:03 +01:00
da6edb199d
gnu: r-xvector: Update to 0.26.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.26.0.
2019-12-15 15:39:02 +01:00
0202b13e8b
gnu: r-genomicranges: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.38.0.
2019-12-15 15:39:02 +01:00
8d1c3666d7
gnu: r-biobase: Update to 2.46.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.46.0.
2019-12-15 15:39:02 +01:00
Tobias Geerinckx-Rice
Marius Bakke
Ricardo Wurmus
Efraim Flashner
Pierre Neidhardt
Brett Gilio
Mădălin Ionel Patrașcu