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2020-01-27gnu: r-gviz: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
2020-01-27gnu: r-genomicfeatures: Update to 1.38.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
2020-01-27gnu: r-s4vectors: Update to 0.24.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
2020-01-27gnu: r-diversitree: Update to 0.9-13.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
2020-01-27gnu: ocaml: Switch to ocaml 4.09 by default.Julien Lepiller
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.
2020-01-21gnu: Use HTTPS for (gnu packages bioinformatics) home pages.Tobias Geerinckx-Rice
* 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.
2020-01-21gnu: r-gage: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
2020-01-21gnu: sra-tools: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
2020-01-21gnu: raxml: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
2020-01-21gnu: prodigal: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
2020-01-21gnu: miso: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
2020-01-21gnu: grit: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code repository as home page.
2020-01-21gnu: express-beta-diversity: Update home page.Tobias Geerinckx-Rice
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.
2020-01-21gnu: dendropy: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
2020-01-21gnu: Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice
* 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.
2020-01-19gnu: edirect: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
2020-01-16gnu: kentutils: Build with OpenSSL 1.0.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to OPENSSL-1.0.
2020-01-16gnu: r-delayedarray: Update to 0.12.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
2020-01-16gnu: r-iranges: Update to 2.20.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
2020-01-16gnu: r-s4vectors: Update to 0.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
2020-01-16gnu: r-biocstyle: Update to 2.14.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
2020-01-09gnu: smithwaterman: Update to 0.0.0-2.2610e25.Efraim Flashner
* 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.
2020-01-09gnu: vcflib: Update to 1.0.1.Efraim Flashner
* 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.
2020-01-09gnu: fastahack: Update to 1.0.0.Efraim Flashner
* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
2020-01-09gnu: Add intervaltree.Efraim Flashner
* gnu/packages/bioinformatics.scm (intervaltree): New variable. (vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
2020-01-09gnu: tabixpp: Update to 1.1.0.Efraim Flashner
* 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.
2020-01-09gnu: bwa: Install static library.Efraim Flashner
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static library.
2020-01-03gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition.Pierre Neidhardt
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.
2019-12-27gnu: r-topgo: Update to 2.38.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27gnu: r-summarizedexperiment: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27gnu: r-delayedarray: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27gnu: r-biocparallel: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27gnu: r-shortread: Update to 1.44.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
2019-12-23gnu: python-bbknn: Update to 1.3.6.Brett Gilio
* 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.
2019-12-23gnu: tophat: Build with GCC 5Mădălin Ionel Patrașcu
* 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>
2019-12-21gnu: fastx-toolkit: Build with GCC 6Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (fastx-toolkit)[native-inputs]: Add gcc-6. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-12-20gnu: r-scater: Update to 1.14.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
2019-12-17gnu: Add libsbml.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libsbml): New variable.
2019-12-17gnu: r-seurat: Update to 3.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
2019-12-16gnu: python-gffutils: Update description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow paragraph and fix spelling of SQLite.
2019-12-16gnu: Add python-gffutils.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-gffutils): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2019-12-16gnu: python-pyfaidx: Update to 0.5.7.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
2019-12-15gnu: r-genefilter: Update to 1.68.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0. [propagated-inputs]: Remove r-s4vectors and add r-biocgenerics.
2019-12-15gnu: r-deseq2: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
2019-12-15gnu: r-dexseq: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
2019-12-15gnu: r-annotationforge: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
2019-12-15gnu: r-rbgl: Update to 1.62.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
2019-12-15gnu: r-gseabase: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
2019-12-15gnu: r-category: Update to 2.52.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
2019-12-15gnu: r-gostats: Update to 2.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
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