summaryrefslogtreecommitdiff
path: root/gnu
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2019-05-10 13:12:07 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-05-10 13:31:03 +0200
commit5865606459d018758be55f31f8fa4b1f849fa74e (patch)
tree032257b9d3881c251a6354567307301046e08e94 /gnu
parent144415391344ca7118268889867a00a5e5b5b466 (diff)
gnu: Add r-rhisat2.
* gnu/packages/bioconductor.scm (r-rhisat2): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioconductor.scm29
1 files changed, 29 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fce157a516..e534b33555 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -24,6 +24,7 @@
#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
@@ -4433,3 +4434,31 @@ at the start or end of each splice variant. The software includes functions
for splice event prediction, quantification, visualization and
interpretation.")
(license license:artistic2.0)))
+
+(define-public r-rhisat2
+ (package
+ (name "r-rhisat2")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhisat2" version))
+ (sha256
+ (base32
+ "1d1gwl8l2z8kzfvkp1s8vfrh6jbq9ha25dplpf9g62qqa8a46hga"))))
+ (properties `((upstream-name . "Rhisat2")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("which" ,which)))
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-sgseq" ,r-sgseq)))
+ (home-page "https://github.com/fmicompbio/Rhisat2")
+ (synopsis "R Wrapper for HISAT2 sequence aligner")
+ (description
+ "This package provides an R interface to the HISAT2 spliced short-read
+aligner by Kim et al. (2015). The package contains wrapper functions to
+create a genome index and to perform the read alignment to the generated
+index.")
+ (license license:gpl3)))