gnu: Add subread.

* gnu/packages/bioinformatics.scm (subread): New variable.
This commit is contained in:
Ricardo Wurmus 2015-04-16 11:19:45 +02:00
parent 44fd6ef137
commit dbf4ed7c91
1 changed files with 39 additions and 0 deletions

View File

@ -1386,6 +1386,45 @@ sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+))) (license license:gpl3+)))
(define-public subread
(package
(name "subread")
(version "1.4.6-p2")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/subread/subread-"
version "-source.tar.gz"))
(sha256
(base32
"06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:make-flags '("-f" "Makefile.Linux")
#:phases
(alist-cons-after
'unpack 'enter-dir
(lambda _ (chdir "src") #t)
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(mkdir-p bin)
(copy-recursively "../bin" bin)))
;; no "configure" script
(alist-delete 'configure %standard-phases)))))
(inputs `(("zlib" ,zlib)))
(home-page "http://bioinf.wehi.edu.au/subread-package/")
(synopsis "Tool kit for processing next-gen sequencing data")
(description
"The subread package contains the following tools: subread aligner, a
general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
features; exactSNP: a SNP caller that discovers SNPs by testing signals
against local background noises.")
(license license:gpl3+)))
(define-public shogun (define-public shogun
(package (package
(name "shogun") (name "shogun")