summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorzimoun <zimon.toutoune@gmail.com>2021-03-15 19:09:03 +0100
committerRicardo Wurmus <rekado@elephly.net>2021-03-15 23:30:26 +0100
commitadf45daae93219a31dbabd8dd80a806cc747aa81 (patch)
tree7378862e4b8e9de1fb9a0798058f1433fce2d345
parentb1a19ab6e28277f0f9c72961be3cf709bd14e6e2 (diff)
gnu: r-rsamtools: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
-rw-r--r--gnu/packages/bioconductor.scm43
-rw-r--r--gnu/packages/bioinformatics.scm43
2 files changed, 43 insertions, 43 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2b7d65023d..c659bdd09e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rsamtools
+ (package
+ (name "r-rsamtools")
+ (version "2.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rsamtools" version))
+ (sha256
+ (base32
+ "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+ (properties
+ `((upstream-name . "Rsamtools")))
+ (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)))))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bitops" ,r-bitops)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+ (synopsis "Interface to samtools, bcftools, and tabix")
+ (description
+ "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+ (license license:expat)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 415210085e..05805d1a8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,49 +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-rsamtools
- (package
- (name "r-rsamtools")
- (version "2.6.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rsamtools" version))
- (sha256
- (base32
- "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
- (properties
- `((upstream-name . "Rsamtools")))
- (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)))))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bitops" ,r-bitops)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
- (synopsis "Interface to samtools, bcftools, and tabix")
- (description
- "This package provides an interface to the @code{samtools},
-@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
-Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
-tab-delimited (tabix) files.")
- (license license:expat)))
-
(define-public r-delayedarray
(package
(name "r-delayedarray")