gnu: Add smithwaterman.

* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
This commit is contained in:
Pierre Neidhardt 2019-05-18 19:26:35 +02:00 committed by Efraim Flashner
parent 62a031afc4
commit 7faa70cf2b
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1 changed files with 31 additions and 0 deletions

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@ -14867,3 +14867,34 @@ mutations from scRNA-Seq data.")
(description "This is a C++ wrapper around the Tabix project which abstracts
some of the details of opening and jumping in tabix-indexed files.")
(license license:expat)))
(define-public smithwaterman
;; TODO: Upgrading smithwaterman breaks FreeBayes.
(let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
(package
(name "smithwaterman")
(version (string-append "0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/smithwaterman/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests to run.
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "smithwaterman" bin))
#t)))))
(home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm")
(description "Implementation of the Smith-Waterman algorithm.")
;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
(license (list license:gpl2 license:expat)))))