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48/54: gnu: r-copyhelper: Move to (gnu packages bioconductor).
From: |
guix-commits |
Subject: |
48/54: gnu: r-copyhelper: Move to (gnu packages bioconductor). |
Date: |
Mon, 31 May 2021 10:03:20 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 36cb01066cc03b2d341b55f21ebba2156518a560
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Fri May 21 22:26:20 2021 +0200
gnu: r-copyhelper: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
---
gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 24 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2a7872c..9118642 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1128,6 +1128,30 @@ average profile and heatmap of peaks binding to TSS
regions, genomic
annotation, distance to TSS, and overlap of peaks or genes.")
(license license:artistic2.0)))
+(define-public r-copyhelper
+ (package
+ (name "r-copyhelper")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
+ (sha256
+ (base32
+ "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+ (properties `((upstream-name . "CopyhelpeR")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/CopyhelpeR/")
+ (synopsis "Helper files for CopywriteR")
+ (description
+ "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10. In addition, it contains a blacklist filter to remove regions that
+display copy number variation. Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+ (license license:gpl2)))
+
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa92ae3..85e586a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8486,32 +8486,6 @@ analysis, variant tools is project based and provides a
whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-copyhelper
- (package
- (name "r-copyhelper")
- (version "1.6.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://bioconductor.org/packages/release/"
- "data/experiment/src/contrib/CopyhelpeR_"
- version ".tar.gz"))
- (sha256
- (base32
- "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
- (properties `((upstream-name . "CopyhelpeR")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/CopyhelpeR/")
- (synopsis "Helper files for CopywriteR")
- (description
- "This package contains the helper files that are required to run the
-Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
-mm10. In addition, it contains a blacklist filter to remove regions that
-display copy number variation. Files are stored as GRanges objects from the
-GenomicRanges Bioconductor package.")
- (license license:gpl2)))
-
(define-public r-copywriter
(package
(name "r-copywriter")
- 25/54: gnu: r-complexheatmap: Move to (gnu packages bioconductor)., (continued)
- 25/54: gnu: r-complexheatmap: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 20/54: gnu: r-annotationhub: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 22/54: gnu: r-affy: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 32/54: gnu: r-ensembldb: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 33/54: gnu: r-mzr: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 34/54: gnu: r-protgenerics: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 43/54: gnu: r-tximport: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 28/54: gnu: r-organismdbi: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 42/54: gnu: r-mutationalpatterns: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 46/54: gnu: r-rhdf5: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 48/54: gnu: r-copyhelper: Move to (gnu packages bioconductor).,
guix-commits <=
- 51/54: gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1., guix-commits, 2021/05/31
- 24/54: gnu: r-gage: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 26/54: gnu: r-genomicfiles: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 27/54: gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 31/54: gnu: r-biovizbase: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 36/54: gnu: r-motifrg: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 39/54: gnu: r-rhtslib: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 23/54: gnu: r-keggrest: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 30/54: gnu: r-vsn: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31
- 35/54: gnu: r-sva: Move to (gnu packages bioconductor)., guix-commits, 2021/05/31