From 8d64e192dc17bd09e21ec952ff73fab8efaf5db6 Mon Sep 17 00:00:00 2001 From: lingnanyuan <1297162327@qq.com> Date: Tue, 28 Nov 2017 02:27:36 -0600 Subject: r-topgo: Create new package. (#6479) --- .../repos/builtin/packages/r-topgo/package.py | 48 ++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-topgo/package.py diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py new file mode 100644 index 0000000000..2eee5ac588 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 RTopgo(RPackage): + """topGO package provides tools for testing GO terms while accounting + for the topology of the GO graph. Different test statistics and + different methods for eliminating local similarities and dependencies + between GO terms can be implemented and applied.""" + + homepage = "https://www.bioconductor.org/packages/topGO/" + url = "https://git.bioconductor.org/packages/topGO" + + version('2.28.0', git='https://git.bioconductor.org/packages/topGO', commit='066a975d460046cce33fb27e74e6a0ebc33fd716') + + depends_on('r@3.4.0:3.4.9') + depends_on('r-dbi', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-sparsem', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-go-db', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-graph', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) -- cgit v1.2.3-70-g09d2