gnu: Add STAR.

* gnu/packages/bioinformatics.scm (star): New variable.
This commit is contained in:
Ricardo Wurmus 2015-02-09 15:38:30 +01:00
parent 346a829a85
commit ce7155d5dd
1 changed files with 49 additions and 0 deletions

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@ -31,6 +31,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages tbb)
#:use-module (gnu packages vim)
#:use-module (gnu packages zip))
(define-public bedtools
@ -349,3 +350,51 @@ algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
(define-public star
(package
(name "star")
(version "2.4.0j")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/alexdobin/STAR/archive/STAR_"
version ".tar.gz"))
(sha256
(base32
"1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
(modules '((guix build utils)))
(snippet
'(substitute* "source/Makefile"
(("/bin/rm") "rm")))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no check target
#:make-flags '("STAR")
#:phases
(alist-cons-after
'unpack 'enter-source-dir (lambda _ (chdir "source"))
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(mkdir-p bin)
(copy-file "STAR" (string-append bin "STAR"))))
(alist-delete
'configure %standard-phases)))))
(native-inputs
`(("vim" ,vim))) ; for xxd
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/alexdobin/STAR")
(synopsis "Universal RNA-seq aligner")
(description
"The Spliced Transcripts Alignment to a Reference (STAR) software is
based on a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays followed
by seed clustering and stitching procedure. In addition to unbiased de novo
detection of canonical junctions, STAR can discover non-canonical splices and
chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))