From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add Infernal. Date: Fri, 2 Sep 2016 15:35:14 +0200 Message-ID: <20160902133514.26930-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:39489) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bfod1-0000hx-In for guix-devel@gnu.org; Fri, 02 Sep 2016 09:35:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bfocy-0002jC-36 for guix-devel@gnu.org; Fri, 02 Sep 2016 09:35:31 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:51643) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bfocx-0002ix-P6 for guix-devel@gnu.org; Fri, 02 Sep 2016 09:35:28 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 14BEB380DDB for ; Fri, 2 Sep 2016 15:35:26 +0200 (CEST) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id nKClKXEMsaoL for ; Fri, 2 Sep 2016 15:35:20 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Fri, 2 Sep 2016 15:35:20 +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" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (infernal): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 08c2545..1652f71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4835,6 +4835,33 @@ data in the form of VCF files.") ;; at https://vcftools.github.io/license.html (license license:lgpl3))) +(define-public infernal + (package + (name "infernal") + (version "1.1.2") + (source (origin + (method url-fetch) + ;; There are no versioned tarballs + (uri (string-append "http://eddylab.org/software/infernal/" + "infernal-" version ".tar.gz")) + (sha256 + (base32 + "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) + (build-system gnu-build-system) + (native-inputs + `(("perl" ,perl))) ; for tests + (home-page "http://eddylab.org/infernal/") + (synopsis "Inference of RNA alignments") + (description "Infernal (\"INFERence of RNA ALignment\") is a tool for +searching DNA sequence databases for RNA structure and sequence similarities. +It is an implementation of a special case of profile stochastic context-free +grammars called @dfn{covariance models} (CMs). A CM is like a sequence +profile, but it scores a combination of sequence consensus and RNA secondary +structure consensus, so in many cases, it is more capable of identifying RNA +homologs that conserve their secondary structure more than their primary +sequence.") + (license license:bsd-3))) + (define-public r-vegan (package (name "r-vegan") -- 2.9.3