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authorRicardo Wurmus <rekado@elephly.net>2022-09-22 23:28:12 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-09-23 00:21:40 +0200
commitcbe8391d7c570a12416acfbfbbb818404d8b9203 (patch)
tree1f7d3b4facfa600649d8aeb5cc73703f5bb38c58
parent2eb7061aa2e299b87f980450e47985b306626ec9 (diff)
gnu: Add mudskipper.
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5015069a1d..9861d84a29 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16229,6 +16229,43 @@ BigWig files, as well as efficient region coverage summary over intervals from
both types of files.")
(license license:expat)))
+(define-public mudskipper
+ (package
+ (name "mudskipper")
+ (version "0.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "mudskipper" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #false ;fail because the "mudskipper" crate cannot be found
+ #:cargo-inputs
+ (("rust-bio" ,rust-bio-0.39)
+ ("rust-bio-types" ,rust-bio-types-0.12)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-coitrees" ,rust-coitrees-0.2)
+ ("rust-env-logger" ,rust-env-logger-0.9)
+ ("rust-fnv" ,rust-fnv-1)
+ ("rust-indicatif" ,rust-indicatif-0.16)
+ ("rust-libradicl" ,rust-libradicl-0.4)
+ ("rust-linecount" ,rust-linecount-0.1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-num-cpus" ,rust-num-cpus-1)
+ ("rust-rust-htslib" ,rust-rust-htslib-0.38))))
+ (native-inputs
+ (list cmake pkg-config))
+ (inputs
+ (list zlib xz))
+ (home-page "https://github.com/OceanGenomics/mudskipper")
+ (synopsis "Convert genomic alignments to transcriptomic BAM/RAD files.")
+ (description "Mudskipper is a tool for projecting genomic alignments to
+transcriptomic coordinates.")
+ (license license:bsd-3)))
+
(define-public r-ascat
(package
(name "r-ascat")