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gnu: r-systempiper: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
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zimoun 2021-03-08 18:58:28 +01:00 committed by Ricardo Wurmus
parent 8957efa8ef
commit df6b3c25bb
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2 changed files with 54 additions and 54 deletions
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54
gnu/packages/bioconductor.scm
View file

@ -1888,6 +1888,60 @@ (define-public r-shortread
ungapped alignment formats.")
(license license:artistic2.0)))
(define-public r-systempiper
(package
(name "r-systempiper")
(version "1.24.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
"0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
("r-assertthat" ,r-assertthat)
("r-batchtools" ,r-batchtools)
("r-biostrings" ,r-biostrings)
("r-deseq2" ,r-deseq2)
("r-dot" ,r-dot)
("r-edger" ,r-edger)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-go-db" ,r-go-db)
("r-gostats" ,r-gostats)
("r-iranges" ,r-iranges)
("r-limma" ,r-limma)
("r-magrittr" ,r-magrittr)
("r-pheatmap" ,r-pheatmap)
("r-rjson" ,r-rjson)
("r-rsamtools" ,r-rsamtools)
("r-rsvg" ,r-rsvg)
("r-shortread" ,r-shortread)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-yaml" ,r-yaml)
("r-variantannotation" ,r-variantannotation)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tgirke/systemPipeR")
(synopsis "Next generation sequencing workflow and reporting environment")
(description
"This R package provides tools for building and running automated
end-to-end analysis workflows for a wide range of @dfn{next generation
sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
Important features include a uniform workflow interface across different NGS
applications, automated report generation, and support for running both R and
command-line software, such as NGS aligners or peak/variant callers, on local
computers or compute clusters. Efficient handling of complex sample sets and
experimental designs is facilitated by a consistently implemented sample
annotation infrastructure.")
(license license:artistic2.0)))
(define-public r-geneplotter
(package
(name "r-geneplotter")

54
gnu/packages/bioinformatics.scm
View file

@ -7387,60 +7387,6 @@ (define-public r-demultiplex
")
(license license:cc0))))
(define-public r-systempiper
(package
(name "r-systempiper")
(version "1.24.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
"0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
("r-assertthat" ,r-assertthat)
("r-batchtools" ,r-batchtools)
("r-biostrings" ,r-biostrings)
("r-deseq2" ,r-deseq2)
("r-dot" ,r-dot)
("r-edger" ,r-edger)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-go-db" ,r-go-db)
("r-gostats" ,r-gostats)
("r-iranges" ,r-iranges)
("r-limma" ,r-limma)
("r-magrittr" ,r-magrittr)
("r-pheatmap" ,r-pheatmap)
("r-rjson" ,r-rjson)
("r-rsamtools" ,r-rsamtools)
("r-rsvg" ,r-rsvg)
("r-shortread" ,r-shortread)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-yaml" ,r-yaml)
("r-variantannotation" ,r-variantannotation)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tgirke/systemPipeR")
(synopsis "Next generation sequencing workflow and reporting environment")
(description
"This R package provides tools for building and running automated
end-to-end analysis workflows for a wide range of @dfn{next generation
sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
Important features include a uniform workflow interface across different NGS
applications, automated report generation, and support for running both R and
command-line software, such as NGS aligners or peak/variant callers, on local
computers or compute clusters. Efficient handling of complex sample sets and
experimental designs is facilitated by a consistently implemented sample
annotation infrastructure.")
(license license:artistic2.0)))
(define-public r-grohmm
(package
(name "r-grohmm")