From 610cd6a170474550dffd8a58eb3651ef10ca7f6e Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 23 Dec 2020 19:06:35 +0100 Subject: gnu: r-ggbio: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here. --- gnu/packages/bioinformatics.scm | 65 ----------------------------------------- 1 file changed, 65 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc483e6f13..512abcd8fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,71 +10484,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3