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2019-04-19gnu: r-seurat: Update to 3.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.0. [propagated-inputs]: Remove r-dosnow, r-dplyr, r-dtw, r-foreach, r-fpc, r-gplots, r-hdf5r, r-hmisc, r-httr, r-lars, r-mixtools, r-reshape2, and r-tidyr; add r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang, r-rsvd, r-scales, and r-sctransform.
2019-04-11gnu: r-genomicfeatures: Update to 1.34.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.8.
2019-04-11gnu: Add python2-checkm-genome.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.
2019-04-11gnu: Add pplacer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2019-04-06gnu: r-ldblock: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.1.
2019-04-06gnu: r-ensembldb: Update to 2.6.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.8.
2019-04-03gnu: r-rcas: Add upstream name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[properties]: Add upstream name.
2019-04-02gnu: pigx-scrnaseq: Use older loompy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace python-loompy with python-loompy-for-pigx-scrnaseq.
2019-04-02gnu: Add python-loompy-for-pigx-scrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): New variable.
2019-04-02gnu: pigx-chipseq: Update to 0.0.40.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.40.
2019-04-02gnu: python-scanpy: Add python-louvain to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Sort inputs and add python-louvain. [arguments]: Do not delete test that depends on louvain.
2019-03-31gnu: Fix descriptions to not use quotes.Efraim Flashner
* gnu/packages/admin.scm (wpa-supplicant-minimal, mingetty, di), * gnu/packages/audio.scm (fil-plugins), * gnu/packages/base.scm (make-ld-wrapper, make-glibc-locales), * gnu/packages/bioinformatics.scm (r-samtools), * gnu/packages/chez.scm (chez-mit), * gnu/packages/commencement.scm (make-gcc-toolchain), * gnu/packages/compression.scm (fastjar), * gnu/packages/cran.scm (r-maps, r-rcpp), * gnu/packages/databases.scm (sparql-query), * gnu/packages/dunst.scm (dunst), * gnu/packages/ftp.scm (ncftp), * gnu/packages/gl.scm (freeglut), * gnu/packages/haskell-check.scm (ghc-tasty-golden), * gnu/packages/haskell.scm (ghc-case-insensitive, ghc-text, ghc-haskell-src, ghc-syb, ghc-deepseq-generics, ghc-network-uri, ghc-rerebase, ghc-zlib), * gnu/packages/image.scm (jbig2dec), * gnu/packages/kde-frameworks.scm (kinit, karchive), * gnu/packages/linux.scm (wireless-tools, perf, module-init-tools, kbd), * gnu/packages/lirc.scm (lirc), * gnu/packages/lisp.scm (uglify-js), * gnu/packages/mate.scm (mate-netbook), * gnu/packages/microcom.scm (microcom), * gnu/packages/music.scm (bristol), * gnu/packages/networking.scm (perl-geo-ip), * gnu/packages/patchutils.scm (patches), * gnu/packages/perl-check.scm (perl-test-more-utf8), * gnu/packages/perl.scm (perl-log-report-optional, perl-file-which, perl-io-tty, perl-log-any, perl-digest-sha1, perl-class-load, perl-regexp-common, perl-module-pluggable, perl-class-modifier), * gnu/packages/python-xyz.scm (python-backports-abc, python-natsort), * gnu/packages/samba.scm (iniparser), * gnu/packages/search.scm (mlocate), * gnu/packages/spice.scm (spice), * gnu/packages/statistics.scm (r-dt, r-lubridate, r-estimability, r-commonmark, r-digest, r-viridislite, r-stringr), * gnu/packages/tex.scm (texlive-latex-changebar), * gnu/packages/version-control.scm (subversion), * gnu/packages/w3m.scm (w3m), * gnu/packages/web.scm (perl-http-parser, perl-plack-middleware-reverseproxy), * gnu/packages/xorg.scm (xkeyboard-config, mkfontdir, xcursor-theme, mkfontscale, xinit, font-alias)[description]: Use @code instead of quotes.
2019-03-29gnu: Add python-bbknn.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn): New variable.
2019-03-27gnu: trim-galore: Add pigz.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz. [arguments]: Embed reference to pigz.
2019-03-27gnu: trim-galore: Fix test for Python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace "configure" phase to skip ill-advised test for Python.
2019-03-27gnu: r-rhdf5lib: Update to 1.4.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.
2019-03-27gnu: r-genomicfeatures: Update to 1.34.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.
2019-03-26gnu: python-scanpy: Update to 1.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4. [source]: Fetch from git. [arguments]: Disable broken tests. [native-inputs]: Add python-pytest. [home-page]: Use HTTPS.
2019-03-26gnu: trim-galore: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1. [arguments]: Adjust patching.
2019-03-26gnu: cutadapt: Update to 2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1. [source]: Fetch from pypi. [native-inputs]: Add python-setuptools-scm.
2019-03-25gnu: r-gkmsvm: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here... * gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
2019-03-25gnu: r-wgcna: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Move from here... * gnu/packages/cran.scm (r-wgcna): ...to here.
2019-03-25gnu: r-optparse: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-optparse): Move from here... * gnu/packages/cran.scm (r-optparse): ...to here.
2019-03-25gnu: r-bookdown: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Move from here... * gnu/packages/cran.scm (r-bookdown): ...to here.
2019-03-25gnu: r-sparql: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sparql): Move from here... * gnu/packages/cran.scm (r-sparql): ...to here.
2019-03-24gnu: r-seqinr: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqinr): Move from here... * gnu/packages/cran.scm (r-seqinr): ...to here.
2019-03-24gnu: r-acsnminer: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here... * gnu/packages/cran.scm (r-acsnminer): ...to here.
2019-03-24gnu: r-phangorn: Update to 2.5.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3.
2019-03-24gnu: r-gqtlstats: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1.
2019-03-24gnu: r-rbgl: Update to 1.58.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2.
2019-03-22gnu: Add starlong.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (starlong): New variable.
2019-03-21gnu: r-diversitree: Update to 0.9-11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
2019-03-21gnu: r-maldiquant: Update to 1.19.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
2019-03-21gnu: r-diversitree: Fix typo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo in package labels.
2019-03-20gnu: r-annotationhub: Update to 2.14.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
2019-03-20gnu: r-genomicfeatures: Update to 1.34.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
2019-03-20gnu: r-variantannotation: Update to 1.28.13.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
2019-03-20gnu: r-category: Update to 2.48.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
2019-03-20gnu: r-dexseq: Update to 1.28.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
2019-03-20gnu: Add adapterremoval.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
2019-03-19gnu: nanopolish: Use python-wrapper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with "python-wrapper" as scripts require "python" executable.
2019-03-19gnu: nanopolish: Remove bundled library sources.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove bundled htslib sources.
2019-03-18gnu: python-biom-format: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove generated C files. [arguments]: Disable second broken test.
2019-03-18gnu: Add bbmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap): New variable.
2019-03-18gnu: blasr: Add home page.Ricardo Wurmus
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC. * gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
2019-03-18gnu: Add arriba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (arriba): New variable.
2019-03-18gnu: Add blasr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr): New variable.
2019-03-18gnu: Add blasr-libcpp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
2019-03-18gnu: Add pbbam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): New variable.
2019-03-15gnu: Add bwa-meth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
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