@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g.,
names in their natural, rather than lexicographic, order.")
(license license:artistic2.0)))
+(define-public r-genomicalignments
+ (package
+ (name "r-genomicalignments")
+ (version "1.26.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicAlignments" version))
+ (sha256
+ (base32
+ "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
+ (properties
+ `((upstream-name . "GenomicAlignments")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/GenomicAlignments")
+ (synopsis "Representation and manipulation of short genomic alignments")
+ (description
+ "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome). This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+ (license license:artistic2.0)))
+
(define-public r-genomicranges
(package
(name "r-genomicranges")
@@ -7849,39 +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-genomicalignments
- (package
- (name "r-genomicalignments")
- (version "1.26.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicAlignments" version))
- (sha256
- (base32
- "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
- (properties
- `((upstream-name . "GenomicAlignments")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (home-page "https://bioconductor.org/packages/GenomicAlignments")
- (synopsis "Representation and manipulation of short genomic alignments")
- (description
- "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome). This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
- (license license:artistic2.0)))
-
(define-public r-rtracklayer
(package
(name "r-rtracklayer")