From 0b117a03c6c2b7e25bc6f091d5fb03c668c93d98 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Fri, 13 Oct 2017 08:45:05 -0500 Subject: [PATCH] r-summarizedexperiment: created new package (#5734) --- .../r-summarizedexperiment/package.py | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-summarizedexperiment/package.py diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py new file mode 100644 index 0000000000..eab3a17442 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/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/llnl/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 RSummarizedexperiment(RPackage): + """The SummarizedExperiment container contains one or more assays, each + represented by a matrix-like object of numeric or other mode. The rows + typically represent genomic ranges of interest and the columns + represent samples.""" + + homepage = "https://bioconductor.org/packages/SummarizedExperiment/" + url = "https://bioconductor.org/packages/3.5/bioc/src/contrib/SummarizedExperiment_1.6.5.tar.gz" + list_url = homepage + + version('1.6.5', '8f7d534e37cfda1e3e145ec7609c61f5') + + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@1.6.5')