From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] gnu: Add hmmer Date: Sun, 21 Jun 2015 20:17:47 +1000 Message-ID: <55868F4B.6060201@uq.edu.au> References: <55867B39.3020207@uq.edu.au> <87zj3tgziz.fsf@elephly.net> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------090001030605070601050505" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:51821) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6cK8-0004bK-Vk for guix-devel@gnu.org; Sun, 21 Jun 2015 06:18:02 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z6cK6-0004pJ-9H for guix-devel@gnu.org; Sun, 21 Jun 2015 06:18:00 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:35416 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6cK5-0004ol-Mk for guix-devel@gnu.org; Sun, 21 Jun 2015 06:17:58 -0400 In-Reply-To: <87zj3tgziz.fsf@elephly.net> 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. --------------090001030605070601050505 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit On 21/06/15 19:51, Ricardo Wurmus wrote: > The version number is also used in other parts of the URL. How about > this instead (not tested): Works just fine - attached. --------------090001030605070601050505 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 d49710b5a87bfdbe3c12222fd7f42f4fc67875e5 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 21 Jun 2015 20:15:31 +1000 Subject: [PATCH] gnu: Add hmmer. * gnu/packages/bioinformatics.scm (hmmer): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dfaff3..bb5f942 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1032,6 +1032,30 @@ 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 license:gpl3+))) + (define-public htseq (package (name "htseq") -- 2.1.4 --------------090001030605070601050505--