From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add GRIT. Date: Fri, 10 Apr 2015 11:06:42 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:39115) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YgUtq-0007Ft-Rl for guix-devel@gnu.org; Fri, 10 Apr 2015 05:06:55 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YgUtm-0000bg-Ov for guix-devel@gnu.org; Fri, 10 Apr 2015 05:06:54 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:47650) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YgUtm-0000bR-Cr for guix-devel@gnu.org; Fri, 10 Apr 2015 05:06:50 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id B6957380875 for ; Fri, 10 Apr 2015 11:06:48 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03s3d3OZPTWU for ; Fri, 10 Apr 2015 11:06:42 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 10 Apr 2015 11:06:42 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-GRIT.patch" 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: Guix-devel >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") + (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) + %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