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2019-05-24gnu: Move Sphinx and friends to (gnu packages sphinx).Marius Bakke
* gnu/packages/python-xyz.scm (python-sphinxcontrib-websupport, python2-sphinxcontrib-websupport, python-sphinx, python2-sphinx, python-sphinx-gallery, python2-sphinx-gallery, python-sphinx-rtd-theme, python2-sphinx-rtd-theme, python-guzzle-sphinx-theme, python2-guzzle-sphinx-theme, python-sphinxcontrib-newsfeed, python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput, python-sphinx-repoze-interface, python2-sphinx-repoze-interface, python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme, python-sphinx-alabaster-theme, python2-sphinx-alabaster-theme, python-sphinx-me, python-sphinxcontrib-svg2pdfconverter): Move to ... (gnu): * gnu/packages/sphinx.scm: ... here. New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly. * gnu/packages/admin.scm, gnu/packages/bioinformatics.scm, gnu/packages/calendar.scm, gnu/packages/cluster.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/elf.scm, gnu/packages/emacs-xyz.scm, gnu/packages/emulators.scm, gnu/packages/finance.scm, gnu/packages/image.scm, gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm, gnu/packages/openstack.scm, gnu/packages/pdf.scm, gnu/packages/python-web.scm, gnu/packages/search.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/tls.scm, gnu/packages/web.scm: Adjust module imports.
2019-05-23gnu: salmon: Update to 0.13.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1. [arguments]: Adjust "do-not-look-for-boost" build phase; adjust "prepare-rapmap" phase; adjust "use-system-libraries" phase. [inputs]: Remove bwa, jellyfish, spdlog-for-salmon. [native-inputs]: Add pkg-config. (spdlog-for-salmon, bwa-for-salmon): Remove variables.
2019-05-22gnu: umi-tools: Fix typo "containing".Vagrant Cascadian
* gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
2019-05-22gnu: r-gage: Fix typo "functions".Vagrant Cascadian
* gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
2019-05-20gnu: r-limma: Update to 3.40.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
2019-05-20gnu: r-edger: Update to 3.26.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
2019-05-20gnu: r-scater: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
2019-05-20gnu: r-seurat: Update to 3.0.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
2019-05-20gnu: r-maldiquant: Update to 1.19.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
2019-05-20gnu: r-edger: Update to 3.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
2019-05-16gnu: star: Update to 2.7.1a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.7.1a.
2019-05-14gnu: Add ataqv.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ataqv): New variable.
2019-05-11gnu: r-hdf5array: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.1.
2019-05-06gnu: r-systempiper: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0. [propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
2019-05-06gnu: r-rsamtools: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0. [propagated-inputs]: Add r-rhtslib.
2019-05-06gnu: r-impute: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0. [inputs]: Move gfortran from here... [native-inputs]: ...to here.
2019-05-06gnu: r-rcas: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0. [propagated-inputs]: Add ghc-pandoc.
2019-05-06gnu: r-methylkit: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0. [propagated-inputs]: Add r-mgcv.
2019-05-06gnu: r-annotationhub: Update to 2.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0. [propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
2019-05-06gnu: r-fastseg: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
2019-05-06gnu: r-keggrest: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
2019-05-06gnu: r-gage: Update to 2.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
2019-05-06gnu: r-genomicfiles: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
2019-05-06gnu: r-complexheatmap: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0. [propagated-inputs]: Add r-clue and r-png.
2019-05-06gnu: r-dirichletmultinomial: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
2019-05-06gnu: r-ensembldb: Update to 2.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
2019-05-06gnu: r-organismdbi: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
2019-05-06gnu: r-biovizbase: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
2019-05-06gnu: r-ggbio: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
2019-05-06gnu: r-gqtlbase: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
2019-05-06gnu: r-snpstats: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
2019-05-06gnu: r-erma: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
2019-05-06gnu: r-ldblock: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
2019-05-06gnu: r-gqtlstats: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
2019-05-06gnu: r-gviz: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
2019-05-06gnu: r-gwascat: Update to 2.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0. [propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats, r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
2019-05-06gnu: r-sushi: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
2019-05-06gnu: r-fithic: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
2019-05-06gnu: r-hitc: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
2019-05-06gnu: r-hdf5array: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0. [inputs]: Add zlib. [propagated-inputs]: Add r-rhdf5lib.
2019-05-06gnu: r-rhdf5lib: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
2019-05-06gnu: r-beachmat: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.0.0. [inputs]: Remove hdf5 and zlib. [propagated-inputs]: Rmeove r-hdf5array, r-rcpp, r-rhdf5, and r-rhdf5lib.
2019-05-06gnu: r-singlecellexperiment: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.6.0.
2019-05-06gnu: r-scater: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.0. [propagated-inputs]: Add r-biocneighbors and r-biocsingular; remove r-plyr, r-reshape2, and r-rhdf5lib.
2019-05-06gnu: r-scran: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.0. [propagated-inputs]: Add r-bh, r-biocsingular, and r-dqrng; remove r-rhdf5lib.
2019-05-06gnu: r-delayedmatrixstats: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.0.
2019-05-06gnu: r-interactivedisplaybase: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.22.0.
2019-05-06gnu: r-edaseq: Update to 2.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.18.0.
2019-05-06gnu: r-deseq: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.36.0.
2019-05-06gnu: r-aroma-light: Update to 3.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.14.0.
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