From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add OrfM. Date: Tue, 9 Jun 2015 16:15:41 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34137) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z2KJl-0001fG-8S for guix-devel@gnu.org; Tue, 09 Jun 2015 10:15:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z2KJh-0005NG-Aj for guix-devel@gnu.org; Tue, 09 Jun 2015 10:15:52 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:60373) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z2KJg-0005Mg-RJ for guix-devel@gnu.org; Tue, 09 Jun 2015 10:15:49 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 57034380A78 for ; Tue, 9 Jun 2015 16:15:47 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id sIfDrImELQ2v for ; Tue, 9 Jun 2015 16:15:41 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 9 Jun 2015 16:15:41 +0200 (CEST) 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 --=-=-= Content-Type: text/plain Hi Guix, attached is a patch based on a slightly edited snippet that came in through the bio-packaging mailing list. ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-OrfM.patch" >From 6cbd193a53f90e798efc4d83f7acb1d3ae51de12 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 9 Jun 2015 16:10:51 +0200 Subject: [PATCH] gnu: Add OrfM. * gnu/packages/bioinformatics.scm (orfm): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8d59768..55b2ff6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1192,6 +1192,27 @@ RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.") (license license:gpl2))) +(define-public orfm + (package + (name "orfm") + (version "0.3.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/wwood/OrfM/releases/download/v" + version "/orfm-" version ".tar.gz")) + (sha256 + (base32 + "00jqvlspj9662ni9r4n1snxfnwkzc02i46g5nk1kwjshi6v3vgg3")))) + (build-system gnu-build-system) + (inputs `(("zlib" ,zlib))) + (synopsis "Simple and not slow open reading frame (ORF) caller") + (description + "An ORF caller finds stretches of DNA that when translated are not +interrupted by stop codons. OrfM finds and prints these ORFs.") + (home-page "https://github.com/wwood/OrfM") + (license license:lgpl3+))) + (define-public python2-pbcore (package (name "python2-pbcore") -- 2.1.0 --=-=-=--