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2020-07-02gnu: r-annotationdbi: Update to 1.50.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
2020-06-30gnu: blast+: Update to 2.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1.
2020-06-28gnu: r-qtl2: Update synopsis, description.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's synopsis. [description]: Same.
2020-06-28gnu: r-qtl2: Update to 0.22-8.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8. [source]: Download from cran.
2020-06-28gnu: r-scater: Update to 1.16.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.
2020-06-28gnu: r-biocviews: Update to 1.56.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.
2020-06-28gnu: r-dexseq: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.
2020-06-23gnu: miniasm: Make sure all phases return #t.Efraim Flashner
* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom 'install phase return #t.
2020-06-23gnu: miniasm: Don't use unstable tarball.Efraim Flashner
* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using git-fetch.
2020-06-22gnu: python-plotly: Update to 4.8.1.Pierre Langlois
But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22gnu: python-pandas: Update to 1.0.5.Pierre Langlois
But also keep version 0.25.3 around for packages requiring an earlier versions, as well as version 0.24.2 for a version with python2. * gnu/packages/python-science.scm (python-pandas): Update to 1.0.5. [arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not delete tests that depend on "moto", they are skipped automatically. [propagated-inputs]: Add python-jinja2. [inputs]: Add xsel and xclip. [native-inputs]: Add xorg-server-for-tests so we can test clipboard support. (python-pandas-0.24): New variable. (python2-pandas): Inherit from python-pandas-0.25. * gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]: Switch to python-pandas-0.25. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22gnu: deeptools: Deprecate in favor of python-deeptools.Pierre Langlois
And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22gnu: r-hdf5array: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
2020-06-22gnu: r-rhdf5: Update to 2.32.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1.
2020-06-22gnu: r-biomart: Update to 2.44.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
2020-06-22gnu: r-genomeinfodb: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2.
2020-06-22gnu: express: Update to 1.5.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (express): Update to 1.5.3. [source]: Fetch from Github. [arguments]: Add phase "remove-update-check".
2020-06-15gnu: r-limma: Update to 3.44.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
2020-06-13gnu: r-mzr: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-delayedmatrixstats: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-scran: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.16.0. [propagated-inputs]: Add r-iranges. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-scater: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.1. [propagated-inputs]: Add r-rlang. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-singlecellexperiment: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-beachmat: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rhdf5lib: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.0. [source]: Update snippet. [arguments]: Replace ZLIB variables in Makevars. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-hdf5array: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
2020-06-13gnu: r-hitc: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
2020-06-13gnu: r-fithic: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-sushi: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
2020-06-13gnu: r-gwascat: Update to 2.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.20.1. [propagated-inputs]: Remove r-homo-sapiens; add r-ggplot2. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-gviz: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.32.0. [propagated-inputs]: Add r-ensembldb. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-gqtlstats: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-ldblock: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-erma: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-snpstats: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
2020-06-13gnu: r-gqtlbase: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-ggbio: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biovizbase: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
2020-06-13gnu: r-organismdbi: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
2020-06-13gnu: r-ensembldb: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-dirichletmultinomial: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0.
2020-06-13gnu: r-complexheatmap: Update to 2.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.2. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-genomicfiles: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.24.0.
2020-06-13gnu: r-gage: Update to 2.37.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.37.0.
2020-06-13gnu: r-keggrest: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.28.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-fastseg: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.34.0.
2020-06-13gnu: r-annotationhub: Update to 2.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-interactivedisplaybase: Update to 1.26.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.26.3. [propagated-inputs]: Add r-dt. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-edaseq: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.22.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-deseq: Update to 1.39.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.39.0.
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