48 lines
2.4 KiB
Python
48 lines
2.4 KiB
Python
# Copyright 2013-2024 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.package import *
|
|
|
|
|
|
class RSnprelate(RPackage):
|
|
"""Parallel Computing Toolset for Relatedness and Principal Component
|
|
Analysis of SNP Data.
|
|
|
|
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."""
|
|
|
|
bioc = "SNPRelate"
|
|
|
|
version("1.34.0", commit="27a7c9658b974f9887f48a4a3ed1a7621b141488")
|
|
version("1.32.0", commit="2e8cc807baa74fca5137148b672f3945c36689b2")
|
|
version("1.30.1", commit="baef8a71d3908287a2307768348c02db0720d125")
|
|
version("1.28.0", commit="8fcd837f4627a3bb77cb8d992b2baedd0589d123")
|
|
version("1.24.0", commit="419b13b761ea39a8b1b9bc73097fb0359c59f1c2")
|
|
version("1.18.1", commit="81c581bf76392efdc8ba237ca2e42ca1dba788ca")
|
|
version("1.16.0", commit="0e38e8df4af87dff6c27a23af2867661998c0d85")
|
|
version("1.14.0", commit="9501cbfc411aa320e58654a865fda2e9077977af")
|
|
version("1.12.2", commit="dce2e2b6f36483a9f905bb5df6ae834a9f1136fe")
|
|
version("1.10.2", commit="3f5c4010871df742e7a460586b38ad0c2fd37aeb")
|
|
|
|
depends_on("c", type="build") # generated
|
|
depends_on("cxx", type="build") # generated
|
|
|
|
depends_on("r@2.15:", type=("build", "run"))
|
|
depends_on("r-gdsfmt@1.8.3:", type=("build", "run"))
|