r-snprelate: new package (#7036)

1 files changed, 52 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
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+++ b/var/spack/repos/builtin/packages/r-snprelate/package.py
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+##############################################################################
+# 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'))