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Author SHA1 Message Date
Ricardo Wurmus
f73b75e00c
gnu: r-hdf5array: Update to 1.14.3. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
 2020-03-01 23:37:58 +01:00
Ricardo Wurmus
6c1f5a1b7e
gnu: r-rsamtools: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
 2020-03-01 23:37:52 +01:00
Ricardo Wurmus
9bbf3f9de2
gnu: r-edger: Update to 3.28.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
 2020-03-01 23:37:40 +01:00
Ricardo Wurmus
e3eb7ee474
gnu: r-seurat: Update to 3.1.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
 2020-03-01 23:21:17 +01:00
Ricardo Wurmus
643d90bf74
gnu: infernal: Update to 1.1.3. 
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
 2020-02-27 18:18:34 +01:00
Ricardo Wurmus
e6cc426fbb
gnu: vcftools: Update to 0.1.16. 
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
 2020-02-27 18:18:34 +01:00
Ricardo Wurmus
6c32e9b4dc
gnu: bedtools: Update to 2.29.2. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
 2020-02-27 17:38:17 +01:00
Ricardo Wurmus
d24b3b0213
gnu: rseqc: Update to 3.0.1. 
* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
 2020-02-27 17:38:17 +01:00
Ricardo Wurmus
146430ea0e
gnu: proteinortho: Update to 6.0.14. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
 2020-02-26 14:07:32 +01:00
Ricardo Wurmus
9207575669
gnu: diamond: Update to 0.9.30. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
 2020-02-26 14:07:32 +01:00
Ricardo Wurmus
b38dd34f40
gnu: crossmap: Update to 0.3.8. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
 2020-02-26 14:07:32 +01:00
Ricardo Wurmus
640d910427
gnu: macs: Update to 2.2.6. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
 2020-02-26 12:53:23 +01:00
Ricardo Wurmus
59c5f85d06
gnu: Remove python-loompy-for-pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
 2020-02-26 08:59:11 +01:00
Ricardo Wurmus
4f19106770
gnu: pigx-scrnaseq: Update to 1.1.3. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
 2020-02-26 08:58:06 +01:00
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