From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rob Syme Subject: [PATCH] gnu: Add freebayes Date: Mon, 2 May 2016 17:25:50 +0800 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54671) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axA7l-0003wP-0D for guix-devel@gnu.org; Mon, 02 May 2016 05:26:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1axA7Z-0002E8-7N for guix-devel@gnu.org; Mon, 02 May 2016 05:26:35 -0400 Received: from mail-ig0-x243.google.com ([2607:f8b0:4001:c05::243]:33616) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axA7X-0002AP-W2 for guix-devel@gnu.org; Mon, 02 May 2016 05:26:29 -0400 Received: by mail-ig0-x243.google.com with SMTP id rc4so8665932igc.0 for ; Mon, 02 May 2016 02:26:13 -0700 (PDT) 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" To: guix-devel@gnu.org A guix-friendly licensed variant caller. >From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Mon, 2 May 2016 16:46:53 +0800 Subject: [PATCH] gnu: Add freebayes * gnu/packages/bioinformatics.scm (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 079fd46..db382d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cmake) #:use-module (gnu packages curl) #:use-module (gnu packages doxygen) #:use-module (gnu packages datastructures) @@ -1905,6 +1906,44 @@ genes in incomplete assemblies or complete genomes.") ;; GPL3+ according to private correspondense with the authors. (license license:gpl3+))) +(define-public freebayes + (let ((commit "0cb269728b2db6307053cafe6f913a8b6fa1331e")) + (package + (name "freebayes") + (version "1.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit) + (recursive? #t))) + (sha256 + (base32 + "0z37ch3as3g8hx36l1lwy1v9cqahx72lb51yxrcmwymx0kcf39c5")))) + (build-system gnu-build-system) + (arguments '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) ; no "check" target + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "bin/freebayes" bin) + (install-file "bin/bamleftalign" bin) + #t)))))) + (inputs + `(("cmake" ,cmake) + ("zlib" ,zlib))) + (home-page "https://github.com/ekg/freebayes") + (synopsis "Bayesian haplotype-based polymorphism discovery and genotyping") + (description "FreeBayes is a Bayesian genetic variant detector designed to +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat)))) + (define-public fxtract (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) (package -- 2.7.4