From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] gnu: Add metabat. Date: Sat, 11 Jul 2015 16:51:55 +1000 Message-ID: <55A0BD0B.1020306@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------010903010606020108060206" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58277) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZDodv-0008Ky-8T for guix-devel@gnu.org; Sat, 11 Jul 2015 02:52:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZDodq-0004Ad-8m for guix-devel@gnu.org; Sat, 11 Jul 2015 02:52:11 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:40708 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZDodp-00049r-Kj for guix-devel@gnu.org; Sat, 11 Jul 2015 02:52:06 -0400 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 t6B6pwKj042673 for ; Sat, 11 Jul 2015 16:51:58 +1000 Received: from [192.168.1.101] ([103.25.181.216]) (authenticated bits=0) by smtp2.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id t6B6pusg062154 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Sat, 11 Jul 2015 16:51:57 +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. --------------010903010606020108060206 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Thanks for fixing the samtools headers Ricardo, needed that for this. --------------010903010606020108060206 Content-Type: text/x-patch; name="0001-gnu-Add-metabat.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-metabat.patch" >From 3f253f059edee5ee2fdb116e310ab210646acf40 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 11 Jul 2015 16:49:30 +1000 Subject: [PATCH] gnu: Add metabat. * gnu/packages/bioinformatics.scm (metabat): New variable. --- gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a28832d..a349d39 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1394,6 +1394,78 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public metabat + (package + (name "metabat") + (version "0.26.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://bitbucket.org/berkeleylab/metabat/get/" + version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; tests run as part of build phase + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* _ + (substitute* "SConstruct" ; Do not distribute README + (("env.Install.idir_prefix, 'README.md'.") "")) + #t)) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "SConstruct" + (("/include/bam/bam.h") + "/include/samtools/bam.h")) + (substitute* "src/BamUtils.h" + (("#include .bam/bam.h.") + "#include \"samtools/bam.h\"")) + (substitute* "src/BamUtils.h" + (("#include .bam/sam.h.") + "#include \"samtools/sam.h\"")) + (substitute* "src/KseqReader.h" + (("#include \"bam/kseq.h\"") + "#include \"samtools/kseq.h\"")) + (mkdir (assoc-ref outputs "out")) + (zero? (system* "scons" + (string-append + "PREFIX=" + (assoc-ref outputs "out")) + (string-append + "HTSLIB_DIR=" + (assoc-ref inputs "htslib")) + (string-append + "SAMTOOLS_DIR=" + (assoc-ref inputs "samtools")) + (string-append + "BOOST_ROOT=" + (assoc-ref inputs "boost")) + "install")))) + (delete 'install)))) + (inputs + `(("zlib" ,zlib) + ("perl" ,perl) + ("samtools" ,samtools) + ("htslib" ,htslib))) + (native-inputs + `(("boost" ,boost) + ("scons" ,scons))) + (home-page "https://bitbucket.org/berkeleylab/metabat") + (synopsis "Reconstruction of single genomes from complex microbial communities") + (description + "Grouping large genomic fragments assembled from shotgun metagenomic +sequences to deconvolute complex microbial communities, or metagenome binning, +enables the study of individual organisms and their interactions. MetaBAT is +an automated metagenome binning software, which integrates empirical +probabilistic distances of genome abundance and tetranucleotide frequency.") + (license (license:non-copyleft "file://license.txt" + "See LICENSE in the distribution.")))) + (define-public miso (package (name "miso") -- 2.4.3 --------------010903010606020108060206--