53 lines
2.7 KiB
Python
53 lines
2.7 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RSnprelate(RPackage):
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"""Genome-wide association studies (GWAS) are widely used to investigate
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the genetic basis of diseases and traits, but they pose many
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computational challenges. We developed an R package SNPRelate to
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provide a binary format for single-nucleotide polymorphism (SNP) data
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in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files.
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The GDS format offers the efficient operations specifically designed
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for integers with two bits, since a SNP could occupy only two bits.
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SNPRelate is also designed to accelerate two key computations on SNP
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data using parallel computing for multi-core symmetric multiprocessing
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computer architectures: Principal Component Analysis (PCA) and
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relatedness analysis using Identity-By-Descent measures. The SNP GDS
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format is also used by the GWASTools package with the support of S4
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classes and generic functions. The extended GDS format is implemented
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in the SeqArray package to support the storage of single nucleotide
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variations (SNVs), insertion/deletion polymorphism (indel) and
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structural variation calls."""
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homepage = "https://bioconductor.org/packages/SNPRelate"
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git = "https://git.bioconductor.org/packages/SNPRelate.git"
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version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
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depends_on('r@3.4.0:3.4.9', when='@1.12.2')
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depends_on('r-gdsfmt@1.8.3:', type=('build', 'run'))
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