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authorBen Woodcroft <donttrustben@gmail.com>2015-12-10 20:56:52 +1000
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-11 14:34:51 +0100
commit5f7e17bef7083496d590e396324db13708fc6cd7 (patch)
treedeea81b09ef5b01079afead078db712222c477c0 /gnu/packages/bioinformatics.scm
parent9a41f4439d0470bd42d611d5f25bed1bfc6ecc76 (diff)
gnu: Add snap-aligner.
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 17b46752fe..7c573e1626 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2791,6 +2791,43 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
(license license:gpl3)))
+(define-public snap-aligner
+ (package
+ (name "snap-aligner")
+ (version "1.0beta.18")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/amplab/snap/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (install-file "snap-aligner" bin)
+ (install-file "SNAPCommand" bin)
+ #t))))))
+ (native-inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://snap.cs.berkeley.edu/")
+ (synopsis "Short read DNA sequence aligner")
+ (description
+ "SNAP is a fast and accurate aligner for short DNA reads. It is
+optimized for modern read lengths of 100 bases or higher, and takes advantage
+of these reads to align data quickly through a hash-based indexing scheme.")
+ (license license:asl2.0)))
+
(define-public star
(package
(name "star")