From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] gnu: Add hmmer Date: Sun, 21 Jun 2015 18:52:09 +1000 Message-ID: <55867B39.3020207@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------090302080006070207090200" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33988) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6azK-0002jp-6P for guix-devel@gnu.org; Sun, 21 Jun 2015 04:52:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z6azA-00030y-P0 for guix-devel@gnu.org; Sun, 21 Jun 2015 04:52:26 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:52816 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6azA-00030G-5k for guix-devel@gnu.org; Sun, 21 Jun 2015 04:52:16 -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 t5L8qB0K027737 for ; Sun, 21 Jun 2015 18:52:12 +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 t5L8qA9D009656 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Sun, 21 Jun 2015 18:52:11 +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. --------------090302080006070207090200 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit One of my favourite pieces of software. --------------090302080006070207090200 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 7afc66fcf58e75e3738edf31f3cf1da0c1fe4488 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 21 Jun 2015 18:49:56 +1000 Subject: [PATCH] gnu: Add hmmer. * gnu/packages/bioinformatics.scm (hmmer): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dfaff3..a41d0f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1032,6 +1032,29 @@ 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/hmmer3/3.1b2/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 license:gpl3+))) + (define-public htseq (package (name "htseq") -- 2.1.4 --------------090302080006070207090200--