diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9219bc2975..1766855c93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |