gnu: Add r-trackviewer.

* gnu/packages/bioconductor.scm (r-trackviewer): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
This commit is contained in:
Navid Afkhami 2023-09-01 20:45:12 +00:00 committed by Ricardo Wurmus
parent 9f1f80e24b
commit 8c0c94bf9f
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@ -9931,6 +9931,72 @@ (define-public r-tkwidgets
"This package implements widgets to provide user interfaces.") "This package implements widgets to provide user interfaces.")
(license license:artistic2.0))) (license license:artistic2.0)))
(define-public r-trackviewer
(package
(name "r-trackviewer")
(version "1.36.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "trackViewer" version))
(sha256
(base32
"1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))
(snippet
'(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
(properties `((upstream-name . "trackViewer")))
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/htmlwidgets/lib/d3"
(let ((source (assoc-ref inputs "_"))
(target "d3.v4.min.js"))
(format #true "Processing ~a --> ~a~%"
source target)
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))))))))
(propagated-inputs (list r-annotationdbi
r-biocgenerics
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-graph
r-grimport
r-gviz
r-htmlwidgets
r-interactionset
r-iranges
r-plotrix
r-rgraphviz
r-rhdf5
r-rsamtools
r-rtracklayer
r-s4vectors
r-scales
r-strawr))
(native-inputs
(list esbuild
r-knitr
(origin
(method url-fetch)
(uri "https://web.archive.org/web/20230428092426id_/\
https://d3js.org/d3.v4.js")
(sha256
(base32
"0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))
(home-page "https://bioconductor.org/packages/trackViewer")
(synopsis "Web interface for interactive multi-omics data analysis")
(description
"TrackViewer offers multi-omics analysis with web based tracks and
lollipops. Visualize mapped reads along with annotation as track layers for
NGS datasets such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and
methylation data.")
(license license:gpl2+)))
(define-public r-transcriptr (define-public r-transcriptr
(package (package
(name "r-transcriptr") (name "r-transcriptr")