From 0ecef7d7f8bccfcc50429a62342aab214f8e8fb2 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 31 Oct 2017 19:31:06 -0500 Subject: r-somaticsignatures: created new package (#6065) --- .../packages/r-somaticsignatures/package.py | 53 ++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-somaticsignatures/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py new file mode 100644 index 0000000000..355efc3adb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSomaticsignatures(RPackage): + """The SomaticSignatures package identifies mutational signatures of + single nucleotide variants (SNVs). It provides a infrastructure related + to the methodology described in Nik-Zainal (2012, Cell), with + flexibility in the matrix decomposition algorithms.""" + + homepage = "https://bioconductor.org/packages/SomaticSignatures/" + url = "https://git.bioconductor.org/packages/SomaticSignatures" + list_url = homepage + + version('2.12.1', git='https://git.bioconductor.org/packages/SomaticSignatures', commit='932298c6877d076004de5541cec85a14e819517a') + + depends_on('r-variantannotation', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-nmf', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggbio', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-pcamethods', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-proxy', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@2.12.1') -- cgit v1.2.3-60-g2f50