@@ 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+)))