From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add MOSAIK. Date: Fri, 16 Oct 2015 17:43:09 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52286) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Zn7A9-0001jZ-Lc for guix-devel@gnu.org; Fri, 16 Oct 2015 11:43:22 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Zn7A4-0002KC-DA for guix-devel@gnu.org; Fri, 16 Oct 2015 11:43:21 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:57034) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Zn7A3-0002K6-WA for guix-devel@gnu.org; Fri, 16 Oct 2015 11:43:16 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 29F7638068D for ; Fri, 16 Oct 2015 17:43:15 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id yQte6l0gXwIo for ; Fri, 16 Oct 2015 17:43:09 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 16 Oct 2015 17:43:09 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-MOSAIK.patch" 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 >From 2f5755ddad550cf811f97ad6889eea2a7171a1c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Oct 2015 17:41:07 +0200 Subject: [PATCH] gnu: Add MOSAIK. * gnu/packages/bioinformatics.scm (mosaik): New variable. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 069e52f..e339a70 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2248,6 +2248,52 @@ viewer.") (string-append bin "/samtools"))))) (delete 'patch-tests))))))) +(define-public mosaik + (let ((commit "5c25216d")) + (package + (name "mosaik") + (version "2.2.30") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanpinglee/MOSAIK.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ (chdir "src") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-recursively "../bin" bin) + #t)))))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "https://code.google.com/p/mosaik-aligner/") + (synopsis "Map nucleotide sequence reads to reference genomes") + (description + "MOSAIK is a program for mapping second and third-generation sequencing +reads to a reference genome. MOSAIK can align reads generated by all the +major sequencing technologies, including Illumina, Applied Biosystems SOLiD, +Roche 454, Ion Torrent and Pacific BioSciences SMRT.") + ;; MOSAIK is released under the GPLv2+ with the exception of third-party + ;; code released into the public domain: + ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ + ;; 2. MD5 implementation - RSA Data Security, RFC 1321 + (license (list license:gpl2+ license:public-domain))))) + (define-public ngs-sdk (package (name "ngs-sdk") -- 2.1.0