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* gnu: r-genomicranges: Update to 1.40.0.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0. [native-inputs]: Add r-knitr.
* gnu: r-xvector: Update to 0.28.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
* gnu: r-limma: Update to 3.44.1.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
* gnu: r-variantannotation: Update to 1.34.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
* gnu: r-edger: Update to 3.30.3.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
* gnu: r-genomeinfodb: Update to 1.24.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
* gnu: r-iranges: Update to 2.22.2.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
* gnu: r-s4vectors: Update to 0.26.1.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
* gnu: r-bioccheck: Update to 1.24.0.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0. [native-inputs]: Add r-knitr.
* gnu: r-biocstyle: Update to 2.16.0.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0. [native-inputs]: Add r-knitr.
* gnu: r-biocviews: Update to 1.56.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
* gnu: r-grohmm: Update to 1.22.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
* gnu: r-systempiper: Update to 1.22.0.Ricardo Wurmus2020-06-13
| | | | | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0. [propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and r-stringr; remove r-biocgenerics. [native-inputs]: Add r-knitr.
* gnu: r-shortread: Update to 1.46.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
* gnu: r-gostats: Update to 2.54.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
* gnu: r-category: Update to 2.54.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
* gnu: r-gseabase: Update to 1.50.1.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1. [native-inputs]: Add r-knitr.
* gnu: r-rbgl: Update to 1.64.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
* gnu: r-annotationforge: Update to 1.30.1.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1. [native-inputs]: Add r-knitr.
* gnu: r-dexseq: Update to 1.34.0.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0. [native-inputs]: Add r-knitr.
* gnu: r-deseq2: Update to 1.28.1.Ricardo Wurmus2020-06-13
| | | | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1. [propagated-inputs]: Remove r-hmisc. [native-inputs]: Add r-knitr.
* gnu: r-genefilter: Update to 1.70.0.Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0. [native-inputs]: Add r-knitr.
* gnu: r-gprofiler: Move to (gnu packages cran).Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here... * gnu/packages/cran.scm (r-gprofiler): ...to here.
* gnu: rcas-web: Use guile2.2 version of Guile-Redis.Marius Bakke2020-06-06
| | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change from GUILE-REDIS to GUILE2.2-REDIS. While at it, rename the GUILE input to "guile" instead of "guile-next".
* gnu: python-pypairix: Update to 0.3.7 and build programs.Ricardo Wurmus2020-06-04
| | | | | | * gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7. [source]: Fetch from github. [arguments]: Add phases "build-programs" and "install-programs".
* gnu: Add python-pairtools.Ricardo Wurmus2020-06-03
| | | | * gnu/packages/bioinformatics.scm (python-pairtools): New variable.
* gnu: Remove bedtools-2.26.Ricardo Wurmus2020-06-03
| | | | * gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
* gnu: python-pybedtools: Disable unreliable test.Ricardo Wurmus2020-06-03
| | | | | | | * gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable test_intron_exon_reads test; run tests verbosely. test_intron_exon_reads
* gnu: blast+: Use HTTPS home page URI.Nicolas Goaziou2020-05-27
| | | | * gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI.
* gnu: bbmap: Use HTTPS home page URI.Nicolas Goaziou2020-05-27
| | | | * gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI.
* gnu: sra-tools: Update to 2.10.6.Ricardo Wurmus2020-05-19
| | | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6. [arguments]: Replace CC variable in utf8proc Makefile. [inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
* gnu: ncbi-vdb: Update to 2.10.6.Ricardo Wurmus2020-05-19
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6.
* gnu: ngs-sdk: Update to 2.10.5.Ricardo Wurmus2020-05-19
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5.
* Merge branch 'master' into core-updatesMarius Bakke2020-05-05
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| * gnu: Add grocsvs.Efraim Flashner2020-05-05
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (grocsvs): New variable. * gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-30
|\| | | | | | | | | | | | | | | | | | | | | | | | | Conflicts: gnu/local.mk gnu/packages/backup.scm gnu/packages/emacs-xyz.scm gnu/packages/guile.scm gnu/packages/lisp.scm gnu/packages/openldap.scm gnu/packages/package-management.scm gnu/packages/web.scm gnu/packages/xorg.scm
| * gnu: Add miniasm.Roel Janssen2020-04-30
| | | | | | | | * gnu/packages/bioinformatics.scm (miniasm): New variable.
| * gnu: python2-warpedlmm: Fix build.Ricardo Wurmus2020-04-30
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add python2-weave. [arguments]: Disable tests and add "use-weave" phase.
| * gnu: Add variant-tools.Ricardo Wurmus2020-04-28
| | | | | | | | * gnu/packages/bioinformatics.scm (variant-tools): New variable.
| * gnu: r-hdf5array: Update to 1.14.4.Ricardo Wurmus2020-04-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
| * gnu: r-seurat: Update to 3.1.5.Ricardo Wurmus2020-04-28
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5. [propagated-inputs]: Remove r-metap.
| * gnu: Update minimap2 to 2.17.Roel Janssen2020-04-27
| | | | | | | | * gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
| * gnu: Add python-deeptools.Roel Janssen2020-04-27
| | | | | | | | * gnu/packages/bioinformatics.scm (python-deeptools): New variable.
| * gnu: Add python-deeptoolsintervals.Roel Janssen2020-04-27
| | | | | | | | * gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
| * gnu: python-scanpy: Update to 1.4.6.Efraim Flashner2020-04-26
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6. [arguments]: Add another network based test to skip. [propagated-inputs]: Add python-tqdm.
* | Merge branch 'master' into core-updatesMarius Bakke2020-04-19
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| * gnu: python-pygenometracks: Update to 3.3.Ricardo Wurmus2020-04-17
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3. [arguments]: Add phase "relax-requirements"; disable tests. [propagated-inputs]: Remove python-configparser and python-hicexplorer; add python-gffutils, python-pysam, and python-tqdm.
| * gnu: Add python-hicmatrix.Ricardo Wurmus2020-04-17
| | | | | | | | * gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
| * gnu: python-cooler: Update to 0.8.7.Ricardo Wurmus2020-04-17
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7. [propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and python-simplejson. [native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add python-pytest.
| * gnu: python-pybigwig: Update to 0.3.17.Ricardo Wurmus2020-04-17
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
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