From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add aragorn. Date: Tue, 21 Jul 2015 23:55:06 +1000 Message-ID: <55AE4F3A.1050903@uq.edu.au> References: <55AE4599.5040601@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------060202090902030005050702" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55111) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZHY0t-0006P7-1b for guix-devel@gnu.org; Tue, 21 Jul 2015 09:55:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZHY0n-00009w-Fd for guix-devel@gnu.org; Tue, 21 Jul 2015 09:55:19 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:52661 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZHY0m-00007r-Sh for guix-devel@gnu.org; Tue, 21 Jul 2015 09:55:13 -0400 In-Reply-To: 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: Ricardo Wurmus Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------060202090902030005050702 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit On 21/07/15 23:40, Ricardo Wurmus wrote: > Other than that it looks fine to me! Thanks! Ta. Fixed those two things plus some grammar in the description. --------------060202090902030005050702 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 4ac97beef55a5321a9990244ebfcdde38051ff9a Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 21 Jul 2015 23:52:31 +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..8028b49 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")) + (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, mitochondrial RNA and +transfer-messenger RNA from nucleotide sequences, based on homology to known +tRNA consensus sequences and RNA structure. It also outputs the secondary +structure of the predicted RNA.") + (license license:gpl2))) + (define-public bamtools (package (name "bamtools") -- 2.4.3 --------------060202090902030005050702--