From 95ae898345774f6bb26ce11a340b688118d6c4ba Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 16 Jan 2016 14:31:25 +1000 Subject: [PATCH] gnu: Add cd-hit. * gnu/packages/bioinformatics.scm (cd-hit): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a72765a..87b2519 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -807,6 +807,46 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for multiple sequence alignments.") (license license:expat))) +(define-public cd-hit + (package + (name "cd-hit") + (version "4.6.4") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/weizhongli/cdhit/releases/download/V" + version + "/cd-hit-v" + version + "-2015-0603.tar.gz")) + (sha256 + (base32 + "0b6r52hhz3apx3wbc3zpzmxzyv6p7n3w4x3didadsjbnnav5006a")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags + (list (string-append "PREFIX=" + (assoc-ref %outputs "out") + "/bin")) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'install 'create-output-directory + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append + (assoc-ref outputs "out") "/bin"))))))) + (inputs + `(("perl" ,perl))) + (home-page "http://weizhongli-lab.org/cd-hit/") + (synopsis "Cluster and compare protein or nucleotide sequences") + (description + "CD-HIT is a program for clustering and comparing protein or nucleotide +sequences. CD-HIT is designed to be fast and handle extremely large +databases.") + (license license:gpl2))) + (define-public clipper (package (name "clipper") -- 2.6.3