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authorEfraim Flashner <efraim@flashner.co.il>2020-01-08 12:49:17 +0200
committerEfraim Flashner <efraim@flashner.co.il>2020-01-09 14:30:38 +0200
commit2604ecb3a9fc00c98359ecb6059eacfa6573e515 (patch)
tree64538a96643a6bc7e81600a99bcc07cd874860eb
parent0ab7f6c5f4646ca52d6aa54e0adbb4f8b45f9263 (diff)
gnu: smithwaterman: Update to 0.0.0-2.2610e25.
* 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.
-rw-r--r--gnu/packages/bioinformatics.scm15
1 files changed, 9 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bde4aad785..0e4cb5b1db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14942,11 +14942,10 @@ 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"))
+ (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
(package
(name "smithwaterman")
- (version (string-append "0-1." (string-take commit 7)))
+ (version (git-version "0.0.0" "2" commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -14954,17 +14953,21 @@ some of the details of opening and jumping in tabix-indexed files.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+ (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests to run.
+ #:make-flags '("libsw.a" "all")
#: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))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib")))
+ (install-file "smithwaterman" bin)
+ (install-file "libsw.a" lib))
#t)))))
(home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm")