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2020-03-11gnu: python-pybedtools: Update to 0.8.1.Efraim Flashner
* 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.
2020-03-11gnu: python-pyfaidx: Update to 0.5.8.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
2020-03-11gnu: Add python2-pyfaidx.Efraim Flashner
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
2020-03-10gnu: java-forester-1.005: Update source URI.Björn Höfling
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI. [native-inputs]: Wrap long line.
2020-03-09gnu: Fix build of python-velocyto.Roel Janssen
* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to native-inputs to make the test suite run succesfully.
2020-03-08gnu: ngless: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08gnu: taxtastic: Update to 0.8.11.Ricardo Wurmus
* 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.
2020-03-07gnu: r-methylkit: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07gnu: r-vsn: Add r-knitr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-06gnu: python-scanpy: Update to 1.4.5.1.Ricardo Wurmus
* 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.
2020-03-03gnu: gess: Use WRAP-SCRIPT.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT. [inputs]: Add guile-3.0 for wrapper.
2020-03-03gnu: gess: Override PYTHONPATH.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH instead of augmenting it.
2020-03-02gnu: r-seqminer: Update to 8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
2020-03-01gnu: r-hdf5array: Update to 1.14.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
2020-03-01gnu: r-rsamtools: Update to 2.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
2020-03-01gnu: r-edger: Update to 3.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
2020-03-01gnu: r-seurat: Update to 3.1.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4. [propagated-inputs]: Add r-patchwork.
2020-02-27gnu: infernal: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3. [native-inputs]: Add python.
2020-02-27gnu: vcftools: Update to 0.1.16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
2020-02-27gnu: bedtools: Update to 2.29.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2. [native-inputs]: Replace python-2 with python-wrapper. [license]: Change to Expat.
2020-02-27gnu: rseqc: Update to 3.0.1.Ricardo Wurmus
* 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.
2020-02-26gnu: 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.
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