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* gnu: gess: Use WRAP-SCRIPT.Ricardo Wurmus2020-03-03
| | | | | * gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT. [inputs]: Add guile-3.0 for wrapper.
* gnu: gess: Override PYTHONPATH.Ricardo Wurmus2020-03-03
| | | | | * gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH instead of augmenting it.
* gnu: r-seqminer: Update to 8.0.Ricardo Wurmus2020-03-02
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
* gnu: r-hdf5array: Update to 1.14.3.Ricardo Wurmus2020-03-01
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
* gnu: r-rsamtools: Update to 2.2.3.Ricardo Wurmus2020-03-01
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
* gnu: r-edger: Update to 3.28.1.Ricardo Wurmus2020-03-01
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
* gnu: r-seurat: Update to 3.1.4.Ricardo Wurmus2020-03-01
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4. [propagated-inputs]: Add r-patchwork.
* gnu: infernal: Update to 1.1.3.Ricardo Wurmus2020-02-27
| | | | | * gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3. [native-inputs]: Add python.
* gnu: vcftools: Update to 0.1.16.Ricardo Wurmus2020-02-27
| | | | * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
* gnu: bedtools: Update to 2.29.2.Ricardo Wurmus2020-02-27
| | | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2. [native-inputs]: Replace python-2 with python-wrapper. [license]: Change to Expat.
* gnu: rseqc: Update to 3.0.1.Ricardo Wurmus2020-02-27
| | | | | | | | | | * 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.
* gnu: proteinortho: Update to 6.0.14.Ricardo Wurmus2020-02-26
| | | | | | | | | | * 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+
* gnu: diamond: Update to 0.9.30.Ricardo Wurmus2020-02-26
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
* gnu: crossmap: Update to 0.3.8.Ricardo Wurmus2020-02-26
| | | | | | | | | * 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.
* gnu: macs: Update to 2.2.6.Ricardo Wurmus2020-02-26
| | | | | | | | * 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.
* gnu: Remove python-loompy-for-pigx-scrnaseq.Ricardo Wurmus2020-02-26
| | | | | * gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable.
* gnu: pigx-scrnaseq: Update to 1.1.3.Ricardo Wurmus2020-02-26
| | | | | | | * 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.
* gnu: jamm: Update to 1.0.7.6.Ricardo Wurmus2020-02-25
| | | | * gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
* gnu: r-scran: Update to 1.14.6.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
* gnu: r-hdf5array: Update to 1.14.2.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
* gnu: r-gviz: Update to 1.30.3.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
* gnu: r-rhtslib: Update to 1.18.1.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
* gnu: r-genomicfeatures: Update to 1.38.2.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
* gnu: r-rsamtools: Update to 2.2.2.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
* gnu: r-limma: Update to 3.42.2.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
* gnu: r-shortread: Update to 1.44.3.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
* gnu: r-seurat: Update to 3.1.3.Ricardo Wurmus2020-02-19
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3. [propagated-inputs]: Remove r-sdmtools.
* gnu: r-qtl: Update to 1.45-11.Ricardo Wurmus2020-02-19
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
* gn: edirect: Update to 12.1.20190829.Efraim Flashner2020-02-18
| | | | | | The previous version has disappeared upstream. * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
* gnu: python2-pbcore: Remove python2-sphinx dependency.Marius Bakke2020-02-13
| | | | | * gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases. [native-inputs]: Remove PYTHON2-SPHINX.
* gnu: r-gviz: Update to 1.30.1.Ricardo Wurmus2020-01-27
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
* gnu: r-genomicfeatures: Update to 1.38.1.Ricardo Wurmus2020-01-27
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
* gnu: r-s4vectors: Update to 0.24.3.Ricardo Wurmus2020-01-27
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
* gnu: r-diversitree: Update to 0.9-13.Ricardo Wurmus2020-01-27
| | | | * gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
* gnu: ocaml: Switch to ocaml 4.09 by default.Julien Lepiller2020-01-27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: Use HTTPS for (gnu packages bioinformatics) home pages.Tobias Geerinckx-Rice2020-01-21
| | | | | | | | * 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.
* gnu: r-gage: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
* gnu: sra-tools: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
* gnu: raxml: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
* gnu: prodigal: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
* gnu: miso: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
* gnu: grit: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | | * gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code repository as home page.
* gnu: express-beta-diversity: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | | | | | 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.
* gnu: dendropy: Update home page.Tobias Geerinckx-Rice2020-01-21
| | | | * gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
* gnu: Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice2020-01-21
| | | | | | | | * 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.
* gnu: edirect: Use HTTPS home page.Tobias Geerinckx-Rice2020-01-19
| | | | * gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
* gnu: kentutils: Build with OpenSSL 1.0.Marius Bakke2020-01-16
| | | | | * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to OPENSSL-1.0.
* gnu: r-delayedarray: Update to 0.12.2.Ricardo Wurmus2020-01-16
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
* gnu: r-iranges: Update to 2.20.2.Ricardo Wurmus2020-01-16
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
* gnu: r-s4vectors: Update to 0.24.2.Ricardo Wurmus2020-01-16
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
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