From 92b20bfdba8709df8610232b402ef5296eaafa16 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 23 Jan 2018 02:43:22 -0600 Subject: r-snprelate: new package (#7036) --- .../repos/builtin/packages/r-snprelate/package.py | 52 ++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-snprelate/package.py 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..5b026a5831 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2013-2017, 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" + url = "https://git.bioconductor.org/packages/SNPRelate" + + version('1.12.2', git='https://git.bioconductor.org/packages/SNPRelate', 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')) -- cgit v1.2.3-60-g2f50