From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:26:20 +0200 [thread overview]
Message-ID: <20210521202622.26591-48-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>
* 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 f224a5ecb4..eee1561c1b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.")
chromstaR package.")
(license license:gpl3)))
+(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 3ee3d9d4f3..2acca0c055 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,32 +8312,6 @@ 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")
--
2.30.1
next prev parent reply other threads:[~2021-05-21 20:33 UTC|newest]
Thread overview: 52+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-05-21 20:21 [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 04/50] gnu: r-topgo: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 05/50] gnu: r-bsgenome: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 06/50] gnu: r-msnid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 07/50] gnu: r-msnbase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 08/50] gnu: r-samr: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 09/50] gnu: r-impute: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 10/50] gnu: r-seqpattern: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 11/50] gnu: r-go-db: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 12/50] gnu: r-genomation: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 13/50] gnu: r-genomationdata: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 14/50] gnu: r-pcamethods: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 15/50] gnu: r-mzid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 16/50] gnu: r-aroma-light: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 17/50] gnu: r-deseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 18/50] gnu: r-edaseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 19/50] gnu: r-interactivedisplaybase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 20/50] gnu: r-annotationhub: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 21/50] gnu: r-fastseg: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 22/50] gnu: r-affy: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 23/50] gnu: r-keggrest: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 24/50] gnu: r-gage: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 25/50] gnu: r-complexheatmap: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 26/50] gnu: r-genomicfiles: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 28/50] gnu: r-organismdbi: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 29/50] gnu: r-affyio: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 30/50] gnu: r-vsn: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 31/50] gnu: r-biovizbase: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 32/50] gnu: r-ensembldb: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 33/50] gnu: r-mzr: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 34/50] gnu: r-protgenerics: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 35/50] gnu: r-sva: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 36/50] gnu: r-motifrg: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 37/50] gnu: r-seqlogo: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 38/50] gnu: r-zlibbioc: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 39/50] gnu: r-rhtslib: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 40/50] gnu: r-bamsignals: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 41/50] gnu: r-rcas: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 43/50] gnu: r-tximport: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 45/50] gnu: r-annotationfilter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 46/50] gnu: r-rhdf5: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 47/50] gnu: r-chipseq: " zimoun
2021-05-21 20:26 ` zimoun [this message]
2021-05-21 20:26 ` [bug#48575] [PATCH 49/50] gnu: r-copywriter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 50/50] gnu: r-methylkit: " zimoun
2021-05-31 14:07 ` bug#48575: [PATCH 00/50] Move some Bioconductor packages " Ricardo Wurmus
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