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Diffstat (limited to 'var/spack/repos/builtin/packages/r-snprelate/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/r-snprelate/package.py | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py new file mode 100644 index 0000000000..f7a0d04fa9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +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')) |