From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] gnu: Include CodingQuarry gene predictor Date: Wed, 16 Mar 2016 04:50:23 -0400 Message-ID: <20160316085023.GA14979@jasmine> References: <20160308233937.GB24107@jasmine> <20160309175902.GB30271@solar> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54549) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ag7A0-0006AN-A0 for guix-devel@gnu.org; Wed, 16 Mar 2016 04:50:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ag79v-0002lW-E1 for guix-devel@gnu.org; Wed, 16 Mar 2016 04:50:31 -0400 Received: from out2-smtp.messagingengine.com ([66.111.4.26]:38016) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ag79v-0002lQ-A9 for guix-devel@gnu.org; Wed, 16 Mar 2016 04:50:27 -0400 Content-Disposition: inline In-Reply-To: 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: Rob Syme Cc: guix-devel@gnu.org On Fri, Mar 11, 2016 at 03:55:47AM +0000, Rob Syme wrote: > Dear Guix, > > I have attached the amended patch to add the CodingQuarry gene predictor > (v2.0). Thanks for the kind feedback on my previous patch. I have tried to > make the formatting etc look as close as I can to the other GNU patches, > but let me know if I've missed anything. Thanks! I simplified the install phase a little bit. Install-file does mkdir-p for you, so I removed some extraneous parts. Pushed as 6a35566df7 > > Rob Syme > Research Associate > Pulse Pathology and Genetics > Centre for Crop and Disease Management > Curtin University > > > On Thu, 10 Mar 2016 at 01:59 Andreas Enge wrote: > > > On Tue, Mar 08, 2016 at 06:39:37PM -0500, Leo Famulari wrote: > > > > + (delete 'check) ;; Don't run the 'make check' step of the > > > > gnu-build-system > > > When skippping the tests, we prefer to say why in the comment. It can be > > > as simple as "no test suite" if that is the case. > > > > And use in the argument block: > > #:tests? #f > > instead of deleting the phase. > > > > Andreas > > > > > From 8cc815999e4481d45e503faa77e06053204385f8 Mon Sep 17 00:00:00 2001 > From: Rob Syme > Date: Fri, 11 Mar 2016 11:47:24 +0800 > Subject: [PATCH] gnu: Add CodingQuarry. > > * gnu/packages/bioinformatics.scm (codingquarry): New variable. > --- > gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 43 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index b3d8827..aec16f3 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -957,6 +957,49 @@ also includes an interface for tabix.") > "CLIPper is a tool to define peaks in CLIP-seq datasets.") > (license license:gpl2))) > > +(define-public codingquarry > + (package > + (name "codingquarry") > + (version "2.0") > + (source (origin > + (method url-fetch) > + (uri (string-append > + "mirror://sourceforge/codingquarry/CodingQuarry_v" > + version ".tar.gz")) > + (sha256 > + (base32 > + "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) > + (build-system gnu-build-system) > + (arguments > + '(#:tests? #f ; no "check" target > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let* ((out (assoc-ref outputs "out")) > + (bin (string-append out "/bin")) > + (doc (string-append out "/share/doc/codingquarry"))) > + (mkdir-p bin) > + (mkdir-p doc) > + (copy-file "INSTRUCTIONS.pdf" > + (string-append doc "/INSTRUCTIONS.pdf")) > + (copy-recursively "QuarryFiles" > + (string-append out "/QuarryFiles")) > + (install-file "CodingQuarry" bin) > + (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) > + (inputs `(("openmpi" ,openmpi))) > + (native-search-paths > + (list (search-path-specification > + (variable "QUARRY_PATH") > + (files '("QuarryFiles"))))) > + (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported > + (synopsis "Fungal gene predictor") > + (description "CodingQuarry is a highly accurate, self-training GHMM fungal > +gene predictor designed to work with assembled, aligned RNA-seq transcripts.") > + (home-page "https://sourceforge.net/projects/codingquarry/") > + (license license:gpl3+))) > + > (define-public couger > (package > (name "couger") > -- > 2.5.0 >