From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add SortMeRNA. Date: Fri, 22 Jan 2016 22:12:54 +1000 Message-ID: <56A21CC6.3010906@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------060300070100030509020601" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:53898) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMaaS-0002pE-0Z for guix-devel@gnu.org; Fri, 22 Jan 2016 07:13:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aMaaM-0007pl-VO for guix-devel@gnu.org; Fri, 22 Jan 2016 07:13:07 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:58091 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMaaM-0007pd-EA for guix-devel@gnu.org; Fri, 22 Jan 2016 07:13:02 -0500 Received: from smtp1.soe.uq.edu.au (smtp1.soe.uq.edu.au [10.138.113.40]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id u0MCCvkq031320 for ; Fri, 22 Jan 2016 22:12:57 +1000 Received: from [192.168.1.105] (static.customers.nuskope.com.au [103.25.181.216] (may be forged)) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id u0MCCsc6047905 (version=TLSv1.2 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Fri, 22 Jan 2016 22:12:56 +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. --------------060300070100030509020601 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Thanks in advance as usual. --------------060300070100030509020601 Content-Type: text/x-patch; name="0001-gnu-Add-sortmerna.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-sortmerna.patch" >From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 16 Jan 2016 13:33:08 +1000 Subject: [PATCH] gnu: Add sortmerna. * gnu/packages/bioinformatics.scm (sortmerna): 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 e579afe..e170ff7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3016,6 +3016,45 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.") (license license:asl2.0))) +(define-public sortmerna + (package + (name "sortmerna") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/biocore/sortmerna/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/sortmerna/rRNA_databases"))) + (install-file "sortmerna" bin) + (install-file "indexdb_rna" bin) + (for-each (lambda (file) + (install-file file share)) + (find-files "rRNA_databases" ".*fasta")) + #t)))))) + (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") + (synopsis "Biological sequence analysis tool for NGS reads") + (description + "SortMeRNA is a biological sequence analysis tool for filtering, mapping +and operational taxonomic unit (OTU) picking next generation sequencing reads. +The core algorithm is based on approximate seeds and allows for fast and +sensitive analyses of nucleotide sequences. The main application of SortMeRNA +is filtering rRNA from metatranscriptomic data.") + (license license:lgpl3))) + (define-public star (package (name "star") -- 2.6.3 --------------060300070100030509020601--