eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
34 lines
1.7 KiB
Python
34 lines
1.7 KiB
Python
# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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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