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2018-02-16gnu: diamond: Update to 0.9.18.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
2018-02-14gnu: vsearch: Update to 2.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
2018-02-13gnu: r-gprofiler: Update to 0.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
2018-02-13gnu: r-ensembldb: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
2018-02-13gnu: r-gage: Update to 2.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
2018-02-13gnu: r-keggrest: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
2018-02-13gnu: r-seurat: Update to 2.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0. [propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
2018-02-13gnu: r-msnbase: Update to 2.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
2018-02-13gnu: r-methylkit: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
2018-02-13gnu: r-gkmsvm: Update to 0.79.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
2018-02-13gnu: r-wgcna: Update to 1.62.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
2018-02-13gnu: r-genomation: Update to 1.11.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
2018-02-13gnu: r-genomicfeatures: Update to 1.30.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
2018-02-13gnu: r-rtracklayer: Update to 1.38.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
2018-02-13gnu: r-summarizedexperiment: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
2018-02-13gnu: r-biomart: Update to 2.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
2018-02-13gnu: r-genomicranges: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
2018-02-13gnu: r-limma: Update to 3.34.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
2018-02-13gnu: r-variantannotation: Update to 1.24.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
2018-02-13gnu: r-edger: Update to 3.20.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
2018-02-13gnu: r-bookdown: Update to 0.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6. [propagated-inputs]: Add r-xfun and ghc-pandoc.
2018-02-13gnu: r-vegan: Update to 2.4-6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
2018-02-12gnu: Add r-scran.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): New variable.
2018-02-12gnu: Add r-scater.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): New variable. Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
2018-02-12gnu: Add r-singlecellexperiment.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
2018-02-12gnu: Add r-beachmat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
2018-02-12gnu: Add r-rhdf5lib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
2018-02-11gnu: Add r-hdf5array.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
2018-02-02gnu: diamond: Update to 0.9.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.17.
2018-01-27gnu: diamond: Update to 0.9.16.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.16.
2018-01-26gnu: diamond: Update to 0.9.15.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.15.
2018-01-26gnu: deeptools: Update URI.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (deeptools)[source, home-page]: Update URI.
2018-01-22gnu: star: Make reproducible.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase "make-reproducible".
2018-01-22gnu: khmer: Add aarch64-linux to supported systems.Efraim Flashner
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add aarch64-linux to the supported systems.
2018-01-21gnu: Add salmon.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon, spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
2018-01-21gnu: Add sailfish.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish): New variable.
2018-01-21gnu: Add libdivsufsort.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.
2018-01-21gnu: Add libgff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libgff): New variable.
2018-01-10gnu: seqmagick: Use 'pypi-uri'.Ben Woodcroft
* gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
2018-01-10gnu: mafft: Update to 7.313.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.313. [source]: Use HTTPS URI.
2018-01-09gnu: seqmagick: Update to 0.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0. Use python-3. [arguments]: Remove replacement phase for check. [inputs]: Add biopython. Remove python2-biopython-1.66. (python2-biopython-1.66): Remove variable.
2018-01-02gnu: htslib: Mark up description.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
2018-01-02gnu: ribotaper: Wrap executables.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase "wrap-executables".
2018-01-02gnu: python-pysam: Update to 0.13.0.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.13.0.
2018-01-02gnu: htslib: Update to 1.6.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
2017-12-27gnu: vsearch: Update to 2.6.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.2.
2017-12-24gnu, doc: Use HTTPS for cran.r-project.org home pages.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm) (r-maldiquant, r-gprofiler)[home-page]: Use HTTPS. * gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape) (r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle) (r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim) (r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken) (r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise. * gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab) [home-page]: Likewise. * gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise. * gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign) (r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability) (r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr) (r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports) (r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops) (r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options) (r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel) (r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3) (r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots) (r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools) (r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp) (r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn) (r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]: Likewise. * gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]: Likewise. * doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-22gnu: Update r-mutationalpatterns to 1.4.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
2017-12-19gnu: r-biomart: Update to 2.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1. [propagated-inputs]: Add r-httr.
2017-12-19gnu: r-gviz: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
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