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gnu: r-homo-sapiens: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
This commit is contained in:
zimoun 2020-12-23 19:06:32 +01:00 committed by Ricardo Wurmus
parent 8c2b7c9a2a
commit a2c66d18a5
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GPG key ID: 197A5888235FACAC
2 changed files with 27 additions and 32 deletions
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27
gnu/packages/bioconductor.scm
View file

@ -389,6 +389,33 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
(version "1.3.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Homo.sapiens" version 'annotation))
(sha256
(base32
"151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
(properties
`((upstream-name . "Homo.sapiens")))
(build-system r-build-system)
(propagated-inputs
`(("r-genomicfeatures" ,r-genomicfeatures)
("r-go-db" ,r-go-db)
("r-org-hs-eg-db" ,r-org-hs-eg-db)
("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
("r-organismdbi" ,r-organismdbi)
("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://bioconductor.org/packages/Homo.sapiens/")
(synopsis "Annotation package for the Homo.sapiens object")
(description
"This package contains the Homo.sapiens object to access data from
several related annotation packages.")
(license license:artistic2.0)))
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")

32
gnu/packages/bioinformatics.scm
View file

@ -10623,38 +10623,6 @@ (define-public r-snpstats
the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(license license:gpl3)))
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
(version "1.3.1")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"Homo.sapiens_"
version ".tar.gz"))
(sha256
(base32
"151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
(properties
`((upstream-name . "Homo.sapiens")))
(build-system r-build-system)
(propagated-inputs
`(("r-genomicfeatures" ,r-genomicfeatures)
("r-go-db" ,r-go-db)
("r-org-hs-eg-db" ,r-org-hs-eg-db)
("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
("r-organismdbi" ,r-organismdbi)
("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://bioconductor.org/packages/Homo.sapiens/")
(synopsis "Annotation package for the Homo.sapiens object")
(description
"This package contains the Homo.sapiens object to access data from
several related annotation packages.")
(license license:artistic2.0)))
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))