>From e75aa388931c92657336c8a15f88b6a0273f5e02 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 22 Mar 2016 15:01:37 +0100 Subject: [PATCH 2/8] gnu: Add smithwaterman. * gnu/packages/bioinformatics.scm (smithwaterman): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6792be9..fa7ba24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4830,3 +4830,34 @@ group or two ChIP groups run under different conditions.") (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 + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/smithwaterman/archive/" + commit ".tar.gz")) + (file-name (string-append name "-" version "-checkout.tar.gz")) + (sha256 + (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) + (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))))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "This package provides an implementation of the Smith-Waterman +algorithm.") + ;; libdisorder is licensed GPLv2. The parent project (vcflib), of which + ;; this program is a submodule, is licensed MIT, which is the same as + ;; the Expat license. + (license (list license:gpl2 license:expat))))) -- 2.5.5