| Age | Commit message (Expand) | Author |
|---|
| 2020-02-13 | gnu: python2-pbcore: Remove python2-sphinx dependency....* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
| Marius Bakke |
| 2020-01-27 | gnu: r-gviz: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-genomicfeatures: Update to 1.38.1....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-s4vectors: Update to 0.24.3....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-diversitree: Update to 0.9-13....* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
| Ricardo Wurmus |
| 2020-01-27 | 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.
| Julien Lepiller |
| 2020-01-21 | 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.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: r-gage: Update home page....* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: sra-tools: Update home page....* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: raxml: Update home page....* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: prodigal: Update home page....* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: miso: Update home page....* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: grit: Update home page....* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
| Tobias Geerinckx-Rice |
| 2020-01-21 | 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.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: dendropy: Update home page....* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | 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.
| Tobias Geerinckx-Rice |
| 2020-01-19 | gnu: edirect: Use HTTPS home page....* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
| Tobias Geerinckx-Rice |
| 2020-01-16 | gnu: kentutils: Build with OpenSSL 1.0....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
| Marius Bakke |
| 2020-01-16 | gnu: r-delayedarray: Update to 0.12.2....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
| Ricardo Wurmus |
| 2020-01-16 | gnu: r-iranges: Update to 2.20.2....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
| Ricardo Wurmus |
| 2020-01-16 | gnu: r-s4vectors: Update to 0.24.2....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
| Ricardo Wurmus |
| 2020-01-16 | gnu: r-biocstyle: Update to 2.14.4....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
| Ricardo Wurmus |
| 2020-01-09 | 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.
| Efraim Flashner |
| 2020-01-09 | 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.
| Efraim Flashner |
| 2020-01-09 | gnu: fastahack: Update to 1.0.0....* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
| Efraim Flashner |
| 2020-01-09 | gnu: Add intervaltree....* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
| Efraim Flashner |
| 2020-01-09 | 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.
| Efraim Flashner |
| 2020-01-09 | gnu: bwa: Install static library....* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
| Efraim Flashner |
| 2020-01-03 | 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.
| Pierre Neidhardt |
| 2019-12-27 | gnu: r-topgo: Update to 2.38.1....* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
| Ricardo Wurmus |
| 2019-12-27 | gnu: r-summarizedexperiment: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
| Ricardo Wurmus |
| 2019-12-27 | gnu: r-delayedarray: Update to 0.12.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
| Ricardo Wurmus |
| 2019-12-27 | gnu: r-biocparallel: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
| Ricardo Wurmus |
| 2019-12-27 | gnu: r-shortread: Update to 1.44.1....* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
| Ricardo Wurmus |
| 2019-12-23 | 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.
| Brett Gilio |
| 2019-12-23 | 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>
| Mădălin Ionel Patrașcu |
| 2019-12-21 | 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>
| Mădălin Ionel Patrașcu |
| 2019-12-20 | gnu: r-scater: Update to 1.14.6....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
| Ricardo Wurmus |
| 2019-12-17 | gnu: Add libsbml....* gnu/packages/bioinformatics.scm (libsbml): New variable.
| Ricardo Wurmus |
| 2019-12-17 | gnu: r-seurat: Update to 3.1.2....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
| Ricardo Wurmus |
| 2019-12-16 | gnu: python-gffutils: Update description....* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.
| Ricardo Wurmus |
| 2019-12-16 | gnu: Add python-gffutils....* gnu/packages/bioinformatics.scm (python-gffutils): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2019-12-16 | gnu: python-pyfaidx: Update to 0.5.7....* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
| Mădălin Ionel Patrașcu |
| 2019-12-15 | 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.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-deseq2: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-dexseq: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-annotationforge: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-rbgl: Update to 1.62.1....* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-gseabase: Update to 1.48.0....* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
| Ricardo Wurmus |
| 2019-12-15 | gnu: r-category: Update to 2.52.1....* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
| Ricardo Wurmus |
