7fe746e071
gnu: python-intervaltree: Update to 3.0.2.
...
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
2020-04-05 20:43:17 +02:00
f12f7a0464
gnu: sailfish: Fix build failure.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to
CPLUS_INCLUDE_PATH instead of overriding it.
2020-04-03 19:11:05 +02:00
0be3cc7f89
gnu: r-biomart: Update to 2.42.1.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
2020-04-01 11:15:26 +02:00
c5c6719f92
gnu: r-genomeinfodb: Update to 1.22.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
2020-04-01 11:15:26 +02:00
18af687037
Merge branch 'master' into core-updates
...
Conflicts:
gnu/packages/icu4c.scm
gnu/packages/man.scm
gnu/packages/python-xyz.scm
guix/scripts/environment.scm
guix/scripts/pack.scm
guix/scripts/package.scm
guix/scripts/pull.scm
guix/store.scm
2020-03-27 00:12:15 +01:00
79c395dde3
gnu: Update sambamba to 0.7.1.
...
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
Remove unneeded undead input.
2020-03-26 18:08:27 +01:00
c649d31957
gnu: r-tximport: Update to 1.14.2.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
2020-03-24 11:06:00 +01:00
10d3fbf051
gnu: edirect: Install more programs.
...
* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
2020-03-22 09:53:57 +02:00
7d13a94215
gnu: Add edirect-go-programs.
...
* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
2020-03-22 09:53:57 +02:00
c4d769d359
Merge branch 'master' into core-updates
2020-03-18 19:41:08 +01:00
961d2ee269
Merge branch 'master' into core-updates
2020-03-14 13:13:40 +01:00
57f6ac8d90
gnu: pigx-scrnaseq: Update to 1.1.4.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
2020-03-17 20:29:19 +01:00
bc6bf142d3
gnu: star: Update to 2.7.3a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
2020-03-16 13:59:20 +01:00
aaadd6e2e1
gnu: salmon: Adjust for C_INCLUDE_PATH changes.
...
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to
C_INCLUDE_PATH instead of CPATH.
2020-03-13 00:18:57 +01:00
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
2020-03-12 16:50:23 +02:00
0b692ef2c6
gnu: r-qtl: Update to 1.46-2.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
2020-03-12 15:15:02 +01:00
d9a2a255f9
gnu: python-pybedtools: Update to 0.8.1.
...
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
2020-03-11 16:31:33 +02:00
173053790c
gnu: python-pyfaidx: Update to 0.5.8.
...
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
2020-03-11 15:45:33 +02:00
ea2822d7d6
gnu: Add python2-pyfaidx.
...
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
2020-03-11 15:43:50 +02:00
ec11dcfe69
gnu: java-forester-1.005: Update source URI.
...
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
2020-03-10 23:35:13 +01:00
c0f6446579
gnu: Fix build of python-velocyto.
...
* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
2020-03-09 14:34:41 +01:00
830eac9c27
gnu: ngless: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08 23:37:09 +01:00
46a864e7c1
gnu: taxtastic: Update to 0.8.11.
...
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
2020-03-08 22:50:16 +01:00
d56553edc3
gnu: r-methylkit: Add r-knitr.
...
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07 19:42:34 +01:00
3b7c644569
gnu: r-vsn: Add r-knitr.
...
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-07 19:31:46 +01:00
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
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
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
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
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
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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
2019-12-20 21:26:26 +01:00
595036d9f9
gnu: Add libsbml.
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* 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.
...
* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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
de9ae3e7b1
gnu: r-annotationdbi: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.48.0.
2019-12-15 15:39:02 +01:00
68a9d9f26a
gnu: r-biomart: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.0.
[propagated-inputs]: Add r-biocfilecache, r-openssl, and r-rappdirs; remove
r-rcurl.
2019-12-15 15:39:02 +01:00
5854a4a265
gnu: r-biocparallel: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.0.
2019-12-15 15:39:02 +01:00
15cd3f6ef5
gnu: r-biostrings: Update to 2.54.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.54.0.
2019-12-15 15:39:02 +01:00
e1d681e2af
gnu: r-rsamtools: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.1.
2019-12-15 15:39:02 +01:00
4ada4fb745
gnu: r-delayedarray: Update to 0.12.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.0.
2019-12-15 15:39:02 +01:00
264db038c6
gnu: r-summarizedexperiment: Update to 1.16.0.
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* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.0.
2019-12-15 15:39:02 +01:00
55e515d206
gnu: r-genomicalignments: Update to 1.22.1.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.22.1.
2019-12-15 15:39:01 +01:00
15187da9e7
gnu: r-rtracklayer: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.46.0.
2019-12-15 15:39:01 +01:00
9fec340391
gnu: r-genomicfeatures: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.0.
2019-12-15 15:39:01 +01:00
323f42b2ca
gnu: r-topgo: Update to 2.37.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.37.0.
2019-12-15 15:39:01 +01:00
e3a2b96c80
gnu: r-bsgenome: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.54.0.
2019-12-15 15:39:01 +01:00
bca1c45e4e
gnu: r-impute: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.60.0.
2019-12-15 15:39:01 +01:00
b590742362
gnu: r-seqpattern: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.18.0.
2019-12-15 15:39:01 +01:00
e06b34e8c6
gnu: r-genomation: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.18.0.
2019-12-15 15:39:01 +01:00
a9790190d1
gnu: r-seqlogo: Update to 1.52.0.
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* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.52.0.
2019-12-15 15:39:01 +01:00
a5f9b30338
gnu: r-motifrg: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.30.0.
2019-12-15 15:39:01 +01:00
2f15045400
gnu: r-zlibbioc: Update to 1.32.0.
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* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.32.0.
2019-12-15 15:39:01 +01:00
108c03a8eb
gnu: r-rhtslib: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.0.
[propagated-inputs]: Add curl.
2019-12-15 15:39:01 +01:00
7b6c008960
gnu: r-bamsignals: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.18.0.
2019-12-15 15:39:00 +01:00
f375d74072
gnu: r-rcas: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.12.0.
2019-12-15 15:39:00 +01:00
3964f2c24e
gnu: r-mutationalpatterns: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.12.0.
2019-12-15 15:39:00 +01:00
3a0229eba0
gnu: r-tximport: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.0.
2019-12-15 15:39:00 +01:00
126539d1ae
gnu: r-rhdf5: Update to 2.30.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.30.1.
2019-12-15 15:39:00 +01:00
4e5c217684
gnu: r-pcamethods: Update to 1.78.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.78.0.
2019-12-15 15:39:00 +01:00
589939937d
gnu: r-msnbase: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.12.0.
2019-12-15 15:39:00 +01:00
597aeb8a34
gnu: r-msnid: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.20.0.
2019-12-15 15:39:00 +01:00
3ccf1e3c20
gnu: r-aroma-light: Update to 3.16.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.16.0.
2019-12-15 15:39:00 +01:00
783bbe3ace
gnu: r-deseq: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.38.0.
2019-12-15 15:39:00 +01:00
0a6704e226
gnu: r-edaseq: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.20.0.
2019-12-15 15:38:59 +01:00
2beffcb558
gnu: r-interactivedisplaybase: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.24.0.
2019-12-15 15:38:59 +01:00
6339ea22f1
gnu: r-annotationhub: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.18.0.
[propagated-inputs]: Add r-biocversion.
2019-12-15 15:38:59 +01:00
c21bf901e2
gnu: r-fastseg: Update to 1.32.0.
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* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.32.0.
2019-12-15 15:38:59 +01:00
fedba48bb5
gnu: r-keggrest: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.26.1.
2019-12-15 15:38:59 +01:00
b342b20a24
gnu: r-gage: Update to 2.36.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.36.0.
2019-12-15 15:38:59 +01:00
48c7ee93b7
gnu: r-genomicfiles: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.22.0.
2019-12-15 15:38:59 +01:00
dac706c322
gnu: r-complexheatmap: Update to 2.2.0.
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* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.2.0.
2019-12-15 15:38:59 +01:00
2edb116c1c
gnu: r-dirichletmultinomial: Update to 1.28.0.
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* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.28.0.
2019-12-15 15:38:59 +01:00
e107f3df54
gnu: r-ensembldb: Update to 2.10.2.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.10.2.
2019-12-15 15:38:59 +01:00
e89032667d
gnu: r-organismdbi: Update to 1.28.0.
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* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.28.0.
2019-12-15 15:38:59 +01:00
866810e686
gnu: r-biovizbase: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.34.1.
2019-12-15 15:38:59 +01:00
81600df302
gnu: r-ggbio: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.34.0.
2019-12-15 15:38:58 +01:00
89a41696ab
gnu: r-gqtlbase: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.18.0.
2019-12-15 15:38:58 +01:00
67d4fd523d
gnu: r-erma: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.2.0.
2019-12-15 15:38:58 +01:00
14eb0978a8
gnu: r-snpstats: Update to 1.36.0.
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* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.36.0.
2019-12-15 15:38:58 +01:00
6fff104191
gnu: r-ldblock: Update to 1.16.0.
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* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.16.0.
[propagated-inputs]: Remove r-go-db and r-homo-sapiens.
2019-12-15 15:38:58 +01:00
cfa93a30b4
gnu: r-gqtlstats: Update to 1.18.0.
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* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.18.0.
2019-12-15 15:38:58 +01:00
d57b6b4bae
gnu: r-gviz: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.0.
2019-12-15 15:38:58 +01:00
2e13f10e89
gnu: r-sushi: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.24.0.
2019-12-15 15:38:58 +01:00
28329991b0
gnu: r-gwascat: Update to 2.18.0.
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* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.18.0.
2019-12-15 15:38:58 +01:00
0a16021241
gnu: r-hitc: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.30.0.
2019-12-15 15:38:58 +01:00
8db2915900
gnu: r-fithic: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.12.0.
2019-12-15 15:38:58 +01:00
7557bd0cce
gnu: r-hdf5array: Update to 1.14.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.1.
[propagated-inputs]: Add r-matrix.
2019-12-15 15:38:57 +01:00
1f5d262cfd
gnu: r-rhdf5lib: Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.8.0.
[arguments]: Update patches.
2019-12-15 15:38:57 +01:00
8804e4b48e
gnu: r-beachmat: Update to 2.2.1.
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* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.2.1.
[propagated-inputs]: Add r-matrix.
2019-12-15 15:38:57 +01:00
376f2f35b6
gnu: r-singlecellexperiment: Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.8.0.
2019-12-15 15:38:57 +01:00
bf23416fe1
gnu: r-scater: Update to 1.14.5.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.5.
[propagated-inputs]: Remove r-dplyr.
2019-12-15 15:38:57 +01:00
964634fa44
gnu: r-scran: Update to 1.14.5.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.5.
[propagated-inputs]: Remove r-dynamictreecut.
2019-12-15 15:38:57 +01:00
c81ccd3076
gnu: r-delayedmatrixstats: Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.8.0.
2019-12-15 15:38:57 +01:00
758dfc61ee
gnu: r-mzid: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.24.0.
2019-12-15 15:38:57 +01:00
dc9d4832b9
gnu: r-vsn: Update to 3.54.0.
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* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.54.0.
2019-12-15 15:38:57 +01:00
af87ac3aa7
gnu: r-annotationfilter: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.10.0.
2019-12-15 15:38:57 +01:00
43058ca656
gnu: r-chipseq: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.36.0.
2019-12-15 15:38:57 +01:00
746e1f062e
gnu: r-copywriter: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.18.0.
2019-12-15 15:38:57 +01:00
32f6059635
gnu: r-affy: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.64.0.
2019-12-15 15:38:56 +01:00
51ca216bdf
gnu: r-affyio: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0.
2019-12-15 15:38:56 +01:00
065c305ca5
gnu: r-methylkit: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0.
2019-12-15 15:38:56 +01:00
2a6ce98b17
gnu: r-sva: Update to 3.34.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0.
2019-12-15 15:38:56 +01:00
d12328f9fe
gnu: r-protgenerics: Update to 1.18.0.
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* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.18.0.
2019-12-15 15:38:56 +01:00
3381dc4b5c
gnu: r-mzr: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0.
2019-12-15 15:38:56 +01:00
5a4aab2193
gnu: Add r-qtl2.
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* gnu/packages/bioinformatics.scm (r-qtl2): New variable.
2019-12-10 13:11:44 +02:00
88f06fd015
gnu: Really move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
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* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
javascript module instead of lisp.
2019-12-05 16:23:06 +01:00
d9544d91a6
Revert "gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm."
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This reverts commit ac1ee30f4f
2019-12-05 15:38:52 +01:00
ac1ee30f4f
gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
...
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
javascript module instead of lisp.
2019-12-05 13:48:47 +01:00
33b59c1a3e
Merge branch 'staging'
2019-12-04 20:12:41 +01:00
ec1224a73b
gnu: python-scipy: Move to (gnu packages python-science).
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* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from
here...
* gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here.
* gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm,
gnu/packages/statistics.scm: Adjust module imports.
2019-12-02 15:25:17 +01:00
076527c354
Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm."
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This reverts commit abf43a67d5
2019-11-28 21:09:24 +01:00
abf43a67d5
gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
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* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
2019-11-28 19:36:12 +01:00
0897ad7fac
Merge branch 'master' into staging
2019-11-28 00:38:25 +01:00
Jakub Kądziołka
Marius Bakke
Ricardo Wurmus
Roel Janssen
Efraim Flashner
Björn Höfling
Julien Lepiller
Tobias Geerinckx-Rice
Pierre Neidhardt
Brett Gilio
Mădălin Ionel Patrașcu