From 30aaa374723f0c493d84f0623001ce87174b12a5 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 23 Jan 2018 02:42:10 -0600 Subject: r-gdsfmt: new package (#7035) --- .../repos/builtin/packages/r-gdsfmt/package.py | 47 ++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-gdsfmt/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py new file mode 100644 index 0000000000..4f209d4327 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 RGdsfmt(RPackage): + """This package provides a high-level R interface to CoreArray Genomic + Data Structure (GDS) data files, which are portable across platforms + with hierarchical structure to store multiple scalable array-oriented + data sets with metadata information. It is suited for large-scale + datasets, especially for data which are much larger than the available + random-access memory. The gdsfmt package offers the efficient + operations specifically designed for integers of less than 8 bits, + since a diploid genotype, like single-nucleotide polymorphism (SNP), + usually occupies fewer bits than a byte. Data compression and + decompression are available with relatively efficient random access. + It is also allowed to read a GDS file in parallel with multiple R + processes supported by the package parallel.""" + + homepage = "http://bioconductor.org/packages/gdsfmt/" + url = "https://git.bioconductor.org/packages/gdsfmt" + + version('1.14.1', git='https://git.bioconductor.org/packages/gdsfmt', commit='15743647b7eea5b82d3284858b4591fb6e59959d') + + depends_on('r@3.4.0:3.4.9', when='@1.14.1') -- cgit v1.2.3-60-g2f50