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07/10: gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
From: |
guix-commits |
Subject: |
07/10: gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). |
Date: |
Mon, 15 Mar 2021 09:07:23 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 8d6d75ff392af1d2633a2ffc07f29c5c1da0071c
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Mon Mar 15 14:01:32 2021 +0100
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
gnu/packages/bioinformatics.scm | 23 -----------------------
2 files changed, 20 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68c5ed7..53f025e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3,6 +3,7 @@
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
@@ -391,6 +392,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011)
and stored
in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-genomeinfodbdata
+ (package
+ (name "r-genomeinfodbdata")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
+ (sha256
+ (base32
+ "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
+ (properties
+ `((upstream-name . "GenomeInfoDbData")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
+ (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+ (description "This package contains data for mapping between NCBI taxonomy
+ID and species. It is used by functions in the GenomeInfoDb package.")
+ (license license:artistic2.0)))
+
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36ecf47..25ade2b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,29 +7691,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomeinfodbdata
- (package
- (name "r-genomeinfodbdata")
- (version "1.2.0")
- (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://bioconductor.org/packages/release/"
-
"data/annotation/src/contrib/GenomeInfoDbData_"
- version ".tar.gz"))
- (sha256
- (base32
- "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
- (properties
- `((upstream-name . "GenomeInfoDbData")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
- (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
- (description "This package contains data for mapping between NCBI taxonomy
-ID and species. It is used by functions in the GenomeInfoDb package.")
- (license license:artistic2.0)))
-
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- branch master updated (53dff6a -> bf612ea), guix-commits, 2021/03/15
- 01/10: gnu: r-biocviews: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 04/10: gnu: r-bioccheck: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 06/10: gnu: r-iranges: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 02/10: gnu: r-biocstyle: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 03/10: gnu: r-grohmm: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 05/10: gnu: r-s4vectors: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 09/10: gnu: r-edger: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 07/10: gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).,
guix-commits <=
- 08/10: gnu: r-genomeinfodb: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15
- 10/10: gnu: r-variantannotation: Move to (gnu packages bioconductor)., guix-commits, 2021/03/15