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[bug#48575] [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioc
From: |
zimoun |
Subject: |
[bug#48575] [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor). |
Date: |
Fri, 21 May 2021 22:25:34 +0200 |
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
---
gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 48 ---------------------------------
2 files changed, 48 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4ff82ad0..42a3d1fffc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and
compressed indexed
tab-delimited (tabix) files.")
(license license:expat)))
+(define-public r-rtracklayer
+ (package
+ (name "r-rtracklayer")
+ (version "1.50.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rtracklayer" version))
+ (sha256
+ (base32
+ "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ ((" zlibbioc,") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/rtracklayer")
+ (synopsis "R interface to genome browsers and their annotation tracks")
+ (description
+ "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in). The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+ (license license:artistic2.0)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d0fe1df30..9fb46c0d5d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +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-rtracklayer
- (package
- (name "r-rtracklayer")
- (version "1.50.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rtracklayer" version))
- (sha256
- (base32
- "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-zlib
- (lambda _
- (substitute* "DESCRIPTION"
- ((" zlibbioc,") ""))
- (substitute* "NAMESPACE"
- (("import\\(zlibbioc\\)") ""))
- #t)))))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/rtracklayer")
- (synopsis "R interface to genome browsers and their annotation tracks")
- (description
- "rtracklayer is an extensible framework for interacting with multiple
-genome browsers (currently UCSC built-in) and manipulating annotation tracks
-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
-built-in). The user may export/import tracks to/from the supported browsers,
-as well as query and modify the browser state, such as the current viewport.")
- (license license:artistic2.0)))
-
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
--
2.30.1
- [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor)., zimoun, 2021/05/21
- [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 <=
- [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, 2021/05/21
- [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