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