858e642e4c
gnu: python-scanpy: Update to 1.4.5.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
2020-03-06 09:16:48 +01:00
4d5d07f75c
gnu: gess: Use WRAP-SCRIPT.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
2020-03-03 11:33:58 +01:00
9309fe355e
gnu: gess: Override PYTHONPATH.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
2020-03-03 11:33:58 +01:00
1284df4ef6
gnu: r-seqminer: Update to 8.0.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
2020-03-02 21:53:48 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
72607005e4
gnu: r-gage: Update home page.
...
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
2020-01-21 02:15:32 +01:00
0388046068
gnu: sra-tools: Update home page.
...
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
2020-01-21 02:15:31 +01:00
0eeaf1ac3c
gnu: raxml: Update home page.
...
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
2020-01-21 02:15:31 +01:00
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
030fe2fb7e
gnu: miso: Update home page.
...
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
2020-01-21 02:15:31 +01:00
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
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
568bd2e382
gnu: dendropy: Update home page.
...
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
2020-01-21 02:15:31 +01:00
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
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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
2020-01-16 06:53:31 +01:00
Ricardo Wurmus
Efraim Flashner
Marius Bakke
Julien Lepiller
Tobias Geerinckx-Rice