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Author SHA1 Message Date
Ricardo Wurmus
788de3aec8
gnu: jamm: Update to 1.0.7.6. 
* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
 2020-02-25 15:37:27 +01:00
Ricardo Wurmus
f55084b782
gnu: r-scran: Update to 1.14.6. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
 2020-02-19 23:00:58 +01:00
Ricardo Wurmus
9374f550e6
gnu: r-hdf5array: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
 2020-02-19 23:00:53 +01:00
Ricardo Wurmus
f2b9f41234
gnu: r-gviz: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
 2020-02-19 23:00:48 +01:00
Ricardo Wurmus
3f4f3a7822
gnu: r-rhtslib: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
 2020-02-19 23:00:42 +01:00
Ricardo Wurmus
f0e330d68b
gnu: r-genomicfeatures: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
 2020-02-19 23:00:36 +01:00
Ricardo Wurmus
154babb9c4
gnu: r-rsamtools: Update to 2.2.2. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
 2020-02-19 23:00:31 +01:00
Ricardo Wurmus
e0ca7b3a14
gnu: r-limma: Update to 3.42.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
 2020-02-19 23:00:25 +01:00
Ricardo Wurmus
0f72b7abd8
gnu: r-shortread: Update to 1.44.3. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
 2020-02-19 23:00:20 +01:00
Ricardo Wurmus
f45ada0fc8
gnu: r-seurat: Update to 3.1.3. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
 2020-02-19 20:55:00 +01:00
Ricardo Wurmus
db092c2a90
gnu: r-qtl: Update to 1.45-11. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
 2020-02-19 20:54:45 +01:00
Efraim Flashner
01005f4269
gn: edirect: Update to 12.1.20190829. 
The previous version has disappeared upstream.

* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
 2020-02-18 13:34:20 +02:00
Marius Bakke
bf71edd3df
gnu: python2-pbcore: Remove python2-sphinx dependency. 
* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
 2020-02-13 16:47:22 +01:00
Ricardo Wurmus
94600c3960
gnu: r-gviz: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
 2020-01-27 20:48:36 +01:00
Ricardo Wurmus
c7b98a84d9
gnu: r-genomicfeatures: Update to 1.38.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
 2020-01-27 20:48:36 +01:00
Ricardo Wurmus
caf4290bd8
gnu: r-s4vectors: Update to 0.24.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
 2020-01-27 20:48:36 +01:00
Ricardo Wurmus
c6b4b4e719
gnu: r-diversitree: Update to 0.9-13. 
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
 2020-01-27 16:33:27 +01:00
Julien Lepiller
87858bc526
gnu: ocaml: Switch to ocaml 4.09 by default. 
Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.

* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
 2020-01-27 03:56:06 +01:00
Tobias Geerinckx-Rice
a19fb6a436
gnu: Use HTTPS for (gnu packages bioinformatics) home pages. 
* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
 2020-01-21 02:15:32 +01:00
Tobias Geerinckx-Rice
72607005e4
gnu: r-gage: Update home page. 
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
 2020-01-21 02:15:32 +01:00
Tobias Geerinckx-Rice
0388046068
gnu: sra-tools: Update home page. 
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
0eeaf1ac3c
gnu: raxml: Update home page. 
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
 2020-01-21 02:15:31 +01:00
Tobias Geerinckx-Rice
5832b88c45
gnu: prodigal: Update home page. 
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
 2020-01-21 02:15:31 +01:00
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