From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] gnu: Add hmmer Date: Wed, 24 Jun 2015 11:52:06 +1000 Message-ID: <558A0D46.3020804@uq.edu.au> References: <55867B39.3020207@uq.edu.au> <87zj3tgziz.fsf@elephly.net> <55868F4B.6060201@uq.edu.au> <87egl57zh0.fsf@netris.org> <20150621181131.GA17424@thebird.nl> <87wpywhqej.fsf@elephly.net> <558A09F5.9000404@uq.edu.au> <558A0C5B.7020402@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------040107060106090106010102" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47132) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7ZrP-0008Gl-NL for guix-devel@gnu.org; Tue, 23 Jun 2015 21:52:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z7ZrI-0000BV-OJ for guix-devel@gnu.org; Tue, 23 Jun 2015 21:52:19 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:43451 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7ZrI-0000BQ-4o for guix-devel@gnu.org; Tue, 23 Jun 2015 21:52:12 -0400 In-Reply-To: <558A0C5B.7020402@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: Ricardo Wurmus , Pjotr Prins Cc: guix-devel@gnu.org This is a multi-part message in MIME format. --------------040107060106090106010102 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit On 24/06/15 11:48, Ben Woodcroft wrote: > > On 24/06/15 11:37, Ben Woodcroft wrote: >> Thanks Mark, that's the only change in the attached patch, except >> that "license:" is added too. > Actually I didn't, I'll send an updated patch soon after testing. > Attached, seems all good now. Apologies for sending too many mails about this. --------------040107060106090106010102 Content-Type: text/x-patch; name="0001-gnu-Add-hmmer.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-hmmer.patch" >From 936ad4f76bbb3825ab5c1623285756cf45f8d192 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 24 Jun 2015 11:51:05 +1000 Subject: [PATCH] gnu: Add hmmer. * gnu/packages/bioinformatics.scm (hmmer): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dfaff3..c88c3ab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1032,6 +1032,35 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public hmmer + (package + (name "hmmer") + (version "3.1b2") + (source (origin + (method url-fetch) + (uri (string-append + "http://selab.janelia.org/software/hmmer" + (version-prefix version 1) "/" + version "/hmmer-" version ".tar.gz")) + (sha256 + (base32 + "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) + (build-system gnu-build-system) + (native-inputs `(("perl", perl))) + (home-page "http://hmmer.janelia.org") + (synopsis "Biosequence analysis using profile hidden Markov models") + (description + "HMMER is used for searching sequence databases for homologs of protein +sequences, and for making protein sequence alignments. It implements methods +using probabilistic models called profile hidden Markov models (profile +HMMs).") + (license (list license:gpl3+ + ;; The bundled library 'easel' is distributed + ;; under The Janelia Farm Software License. + (license:non-copyleft + "file://easel/LICENSE" + "See easel/LICENSE in the distribution."))))) + (define-public htseq (package (name "htseq") -- 2.1.4 --------------040107060106090106010102--