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2020-02-26gnu: proteinortho: Update to 6.0.14.Ricardo Wurmus
* 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+
2020-02-26gnu: diamond: Update to 0.9.30.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
2020-02-26gnu: crossmap: Update to 0.3.8.Ricardo Wurmus
* 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.
2020-02-26gnu: macs: Update to 2.2.6.Ricardo Wurmus
* 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.
2020-02-26gnu: Remove python-loompy-for-pigx-scrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable.
2020-02-26gnu: pigx-scrnaseq: Update to 1.1.3.Ricardo Wurmus
* 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.
2020-02-25gnu: jamm: Update to 1.0.7.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
2020-02-19gnu: r-scran: Update to 1.14.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
2020-02-19gnu: r-hdf5array: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
2020-02-19gnu: r-gviz: Update to 1.30.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
2020-02-19gnu: r-rhtslib: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
2020-02-19gnu: r-genomicfeatures: Update to 1.38.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
2020-02-19gnu: r-rsamtools: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
2020-02-19gnu: r-limma: Update to 3.42.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
2020-02-19gnu: r-shortread: Update to 1.44.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
2020-02-19gnu: r-seurat: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3. [propagated-inputs]: Remove r-sdmtools.
2020-02-19gnu: r-qtl: Update to 1.45-11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
2020-02-18gn: edirect: Update to 12.1.20190829.Efraim Flashner
The previous version has disappeared upstream. * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
2020-02-13gnu: python2-pbcore: Remove python2-sphinx dependency.Marius Bakke
* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases. [native-inputs]: Remove PYTHON2-SPHINX.
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.
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