From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Thompson, David" Subject: Re: [PATCH] gnu: Add Infernal. Date: Fri, 2 Sep 2016 09:44:10 -0400 Message-ID: References: <20160902133514.26930-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41721) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bfomo-0005uI-AY for guix-devel@gnu.org; Fri, 02 Sep 2016 09:45:39 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bfomj-0005K1-Gf for guix-devel@gnu.org; Fri, 02 Sep 2016 09:45:37 -0400 Received: from mail-ua0-f193.google.com ([209.85.217.193]:32855) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bfomj-0005GE-BI for guix-devel@gnu.org; Fri, 02 Sep 2016 09:45:33 -0400 Received: by mail-ua0-f193.google.com with SMTP id 49so359947uat.0 for ; Fri, 02 Sep 2016 06:45:11 -0700 (PDT) In-Reply-To: <20160902133514.26930-1-ricardo.wurmus@mdc-berlin.de> 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: Ricardo Wurmus Cc: guix-devel On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus wrote: > * 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 But the version appears in the URL? > + (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 > > LGTM overall. - Dave