From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH} Add cd-hit. Date: Sun, 21 Feb 2016 21:02:16 +1000 Message-ID: <56C99938.40207@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------030603020602080607060903" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41401) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aXRmW-0005Q0-AM for guix-devel@gnu.org; Sun, 21 Feb 2016 06:02:29 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aXRmS-0008Vr-VU for guix-devel@gnu.org; Sun, 21 Feb 2016 06:02:28 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:41472 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aXRmS-0008Vi-CA for guix-devel@gnu.org; Sun, 21 Feb 2016 06:02:24 -0500 Received: from smtp2.soe.uq.edu.au (smtp2.soe.uq.edu.au [10.138.113.41]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id u1LB2IqW037285 for ; Sun, 21 Feb 2016 21:02:18 +1000 Received: from [192.168.1.105] (static.customers.nuskope.com.au [103.25.181.216] (may be forged)) (authenticated bits=0) by smtp2.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id u1LB2Hct031208 (version=TLSv1.2 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Sun, 21 Feb 2016 21:02:18 +1000 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------030603020602080607060903 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Thanks in advance. --------------030603020602080607060903 Content-Type: text/x-patch; name="0001-gnu-Add-cd-hit.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-cd-hit.patch" >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 --------------030603020602080607060903--