From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add aragorn. Date: Tue, 21 Jul 2015 23:14:01 +1000 Message-ID: <55AE4599.5040601@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------030507070900020001030401" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:42550) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZHXNB-0005KP-Fi for guix-devel@gnu.org; Tue, 21 Jul 2015 09:14:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZHXN4-0000CD-G0 for guix-devel@gnu.org; Tue, 21 Jul 2015 09:14:17 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:59592 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZHXN3-0008RQ-UI for guix-devel@gnu.org; Tue, 21 Jul 2015 09:14:10 -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 t6LDE3XL038131 for ; Tue, 21 Jul 2015 23:14:04 +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 t6LDE1Fs056704 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Tue, 21 Jul 2015 23:14:03 +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. --------------030507070900020001030401 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit --------------030507070900020001030401 Content-Type: text/x-patch; name="0001-gnu-Add-aragorn.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-aragorn.patch" >From 12e455874cf563269efc872235738e0ab4848638 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 21 Jul 2015 23:08:58 +1000 Subject: [PATCH] gnu: Add aragorn. * gnu/packages/bioinformatics.scm (aragorn): New variable --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78cd3ce..1d226ca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -54,6 +54,57 @@ #:use-module (gnu packages xml) #:use-module (gnu packages zip)) +(define-public aragorn + (package + (name "aragorn") + (version "1.2.36") + (source (origin + (method url-fetch) + (uri (string-append + "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" + version ".tgz")) + (file-name (string-append name "-" version ".tgz")) + (sha256 + (base32 + "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (zero? (system* "gcc" + "-O3" + "-ffast-math" + "-finline-functions" + "-o" + "aragorn" + (string-append + "aragorn" ,version ".c"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin")) + (man (string-append + (assoc-ref outputs "out") "/share/man/man1"))) + (mkdir-p bin) + (copy-file "aragorn" + (string-append bin "/aragorn")) + (mkdir-p man) + (copy-file "aragorn.1" + (string-append man "/aragorn.1"))) + #t))))) + (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") + (synopsis + "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") + (description + "Aragorn identifies transfer RNA and transfer-messenger RNA sequences from +nucleotide sequences, based on homology to known tRNA consensus sequences and +RNA structure. It output the secondary structure of the predicted RNA.") + (license license:gpl2))) + (define-public bamtools (package (name "bamtools") -- 2.4.3 --------------030507070900020001030401--