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gnu: smithwaterman: Update to 0.0.0-2.2610e25.

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* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25.
[arguments]: Add make-flags to build static library. Adjust custom
'install phase to install static library.
This commit is contained in:
Efraim Flashner 2020-01-08 12:49:17 +02:00
parent 0ab7f6c5f4
commit 2604ecb3a9
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1 changed files with 9 additions and 6 deletions
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gnu/packages/bioinformatics.scm
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@ -14942,11 +14942,10 @@ some of the details of opening and jumping in tabix-indexed files.")
(license license:expat))) (license license:expat)))
(define-public smithwaterman (define-public smithwaterman
;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
(let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
(package (package
(name "smithwaterman") (name "smithwaterman")
(version (string-append "0-1." (string-take commit 7))) (version (git-version "0.0.0" "2" commit))
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -14954,17 +14953,21 @@ some of the details of opening and jumping in tabix-indexed files.")
(commit commit))) (commit commit)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests to run. `(#:tests? #f ; There are no tests to run.
#:make-flags '("libsw.a" "all")
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) ; There is no configure phase. (delete 'configure) ; There is no configure phase.
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (let* ((out (assoc-ref outputs "out"))
(install-file "smithwaterman" bin)) (bin (string-append out "/bin"))
(lib (string-append out "/lib")))
(install-file "smithwaterman" bin)
(install-file "libsw.a" lib))
#t))))) #t)))))
(home-page "https://github.com/ekg/smithwaterman") (home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm") (synopsis "Implementation of the Smith-Waterman algorithm")