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[bug#48575] [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages b
From: |
zimoun |
Subject: |
[bug#48575] [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor). |
Date: |
Fri, 21 May 2021 22:25:45 +0200 |
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 28 ----------------------------
2 files changed, 26 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2be7920770..22b5a6068e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1021,6 +1021,32 @@ chromstaR package.")
genomes and gene ID formats, largely based on the UCSC table browser.")
(license license:lgpl2.0+)))
+(define-public r-genomationdata
+ (package
+ (name "r-genomationdata")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomationData" version 'experiment))
+ (sha256
+ (base32
+ "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+ (properties
+ `((upstream-name . "genomationData")))
+ (build-system r-build-system)
+ ;; As this package provides little more than large data files, it doesn't
+ ;; make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Experimental data for use with the genomation package")
+ (description
+ "This package contains experimental genetic data for use with the
+genomation package. Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+ (license license:gpl3+)))
+
(define-public r-pasilla
(package
(name "r-pasilla")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f8e7b2cab9..87254a9058 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomationdata
- (package
- (name "r-genomationdata")
- (version "1.22.0")
- (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/experiment/src/contrib/"
- "genomationData_" version ".tar.gz"))
- (sha256
- (base32
- "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
- (build-system r-build-system)
- ;; As this package provides little more than large data files, it doesn't
- ;; make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Experimental data for use with the genomation package")
- (description
- "This package contains experimental genetic data for use with the
-genomation package. Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
- (license license:gpl3+)))
-
(define-public r-seqlogo
(package
(name "r-seqlogo")
--
2.30.1
- [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor)., (continued)
- [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 07/50] gnu: r-msnbase: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 09/50] gnu: r-impute: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 11/50] gnu: r-go-db: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor).,
zimoun <=
- [bug#48575] [PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 04/50] gnu: r-topgo: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 16/50] gnu: r-aroma-light: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 23/50] gnu: r-keggrest: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 24/50] gnu: r-gage: Move to (gnu packages bioconductor)., zimoun, 2021/05/21