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##############################################################################
# Copyright (c) 2013-2018, 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/spack/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 RSnprelate(RPackage):
"""Genome-wide association studies (GWAS) are widely used to investigate
the genetic basis of diseases and traits, but they pose many
computational challenges. We developed an R package SNPRelate to
provide a binary format for single-nucleotide polymorphism (SNP) data
in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files.
The GDS format offers the efficient operations specifically designed
for integers with two bits, since a SNP could occupy only two bits.
SNPRelate is also designed to accelerate two key computations on SNP
data using parallel computing for multi-core symmetric multiprocessing
computer architectures: Principal Component Analysis (PCA) and
relatedness analysis using Identity-By-Descent measures. The SNP GDS
format is also used by the GWASTools package with the support of S4
classes and generic functions. The extended GDS format is implemented
in the SeqArray package to support the storage of single nucleotide
variations (SNVs), insertion/deletion polymorphism (indel) and
structural variation calls."""
homepage = "https://bioconductor.org/packages/SNPRelate"
git = "https://git.bioconductor.org/packages/SNPRelate.git"
version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
depends_on('r@3.4.0:3.4.9', when='@1.12.2')
depends_on('r-gdsfmt@1.8.3:', type=('build', 'run'))
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