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.
...
* 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.
...
* 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.
...
* 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
...
* 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
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
Marius Bakke
Ricardo Wurmus
Julien Lepiller
Tobias Geerinckx-Rice
Efraim Flashner
Pierre Neidhardt
Brett Gilio
Mădălin Ionel Patrașcu