From mboxrd@z Thu Jan 1 00:00:00 1970 From: David Thompson Subject: Re: [PATCH] gnu: Add GRIT. Date: Fri, 10 Apr 2015 07:05:43 -0400 Message-ID: <87mw2gdz08.fsf@fsf.org> References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:32885) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YgWl1-0007XR-GU for guix-devel@gnu.org; Fri, 10 Apr 2015 07:06:01 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YgWkt-00062Q-SA for guix-devel@gnu.org; Fri, 10 Apr 2015 07:05:55 -0400 Received: from mail.fsf.org ([208.118.235.13]:59646) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YgWkt-00062K-Jo for guix-devel@gnu.org; Fri, 10 Apr 2015 07:05:47 -0400 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: Ricardo Wurmus , Guix-devel Ricardo Wurmus writes: > From 9d27d88602fe575e0ebf2c0c7841e8aed7aa563c Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Fri, 10 Apr 2015 11:05:45 +0200 > Subject: [PATCH] gnu: Add GRIT. > > * gnu/packages/bioinformatics.scm (grit): New variable. > --- > gnu/packages/bioinformatics.scm | 49 +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 49 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 0b5eccf..d7f6a0f 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -511,6 +511,55 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from > Illumina, Roche 454, and the SOLiD platform.") > (license license:gpl3))) > > +(define-public grit > + (package > + (name "grit") > + (version "2.0.2") > + (source (origin > + (method url-fetch) > + (uri (string-append > + "https://github.com/nboley/grit/archive/" > + version ".tar.gz")) > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 > + "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) > + (build-system python-build-system) > + (arguments > + `(#:python ,python-2 > + #:phases > + (alist-cons-after > + 'unpack 'generate-from-cython-sources > + (lambda* (#:key inputs outputs #:allow-other-keys) > + (delete-file "grit/sparsify_support_fns.c") > + (delete-file "grit/call_peaks_support_fns.c") A comment explaining why these are deleted would be nice. > + (substitute* "setup.py" > + (("Cython.Setup") "Cython.Build") > + (("pyx\", \\]") > + (string-append "pyx\", ], include_dirs = ['" > + (assoc-ref inputs "python-numpy") > + "/lib/python2.7/site-packages/numpy/core/include/" > + "']"))) #t) A comment for this, too, please. I can tell that this is fixing something related to numpy, but I'm not sure why it needs to be done. > + %standard-phases))) > + (inputs > + `(("python-scipy" ,python2-scipy) > + ("python-numpy" ,python2-numpy) > + ("python-pysam" ,python2-pysam) > + ("python-networkx" ,python2-networkx))) > + (native-inputs > + `(("python-cython" ,python2-cython) > + ("python-setuptools" ,python2-setuptools))) > + (home-page "http://grit-bio.org") > + (synopsis "Tool for integrative analysis of RNA-seq type assays") > + (description > + "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify > +full length transcript models. When none of these data sources are available, > +GRIT can be run by providing a candidate set of TES or TSS sites. In > +addition, GRIT can merge in reference junctions and gene boundaries. GRIT can > +also be run in quantification mode, where it uses a provided GTF file and just > +estimates transcript expression.") > + (license license:gpl3+))) > + > (define-public hisat > (package > (name "hisat") > -- > 2.1.0 > > Looks good otherwise. Thanks! -- David Thompson Web Developer - Free Software Foundation - http://fsf.org GPG Key: 0FF1D807 Support the FSF: https://fsf.org/donate