From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add prodigal. Date: Sat, 27 Jun 2015 09:30:40 +1000 Message-ID: <558DE0A0.5020603@uq.edu.au> References: <558DDFB8.4070303@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------050505040804040707020201" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59266) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8d57-0003EJ-Q0 for guix-devel@gnu.org; Fri, 26 Jun 2015 19:30:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z8d54-0003GC-KC for guix-devel@gnu.org; Fri, 26 Jun 2015 19:30:49 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:41658 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8d54-0003Db-0N for guix-devel@gnu.org; Fri, 26 Jun 2015 19:30:46 -0400 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 t5QNUiOi026876 for ; Sat, 27 Jun 2015 09:30:44 +1000 Received: from [192.168.1.101] ([103.25.181.216]) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id t5QNUfCV005550 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Sat, 27 Jun 2015 09:30:43 +1000 In-Reply-To: <558DDFB8.4070303@uq.edu.au> 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. --------------050505040804040707020201 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Oops, now all lines <= 80 chars. On 27/06/15 09:26, Ben Woodcroft wrote: > A popular tool in microbial ecology. --------------050505040804040707020201 Content-Type: text/x-patch; name="0001-gnu-Add-prodigal.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-prodigal.patch" >From 6e81c91c5e444cddf6e193f22d212b1eee3a5cab Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 27 Jun 2015 09:29:23 +1000 Subject: [PATCH] gnu: Add prodigal. * gnu/packages/bioinformatics.scm (prodigal): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31df219..40a7d78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1405,6 +1405,41 @@ files and writing bioinformatics applications.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public prodigal + (package + (name "prodigal") + (version "2.6.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/hyattpd/Prodigal/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "prodigal" (string-append bin "/prodigal")) + #t)))))) + (home-page "http://prodigal.ornl.gov") + (synopsis "Protein-coding gene prediction for Archaea and Bacteria") + (description + "Prodigal runs smoothly on finished genomes, draft genomes, and +metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table +format. It runs quickly, in an unsupervised fashion, handles gaps, handles +partial genes, and identifies translation initiation sites.") + (license license:gpl3+))) + (define-public rsem (package (name "rsem") -- 2.4.3 --------------050505040804040707020201--