From: zimoun <zimon.toutoune@gmail.com>
To: 45399@debbugs.gnu.org
Subject: [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:32 +0100 [thread overview]
Message-ID: <20201223180635.58647-8-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com>
* 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'.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 32 --------------------------------
2 files changed, 27 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 466bb71101..3b8dce30e5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
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")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c59d7a690..2a6ac38505 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10623,38 +10623,6 @@ and more.")
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"))
--
2.29.2
next prev parent reply other threads:[~2020-12-23 18:07 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-12-23 18:03 [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
2020-12-23 18:06 ` zimoun [this message]
2020-12-23 18:06 ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 10/10] gnu: r-ggbio: " zimoun
2020-12-29 16:42 ` bug#45399: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2020-12-30 9:13 ` [bug#45399] " zimoun
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