r-dose: Create new package. (#6355)

1 files changed, 52 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-dose/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 RDose(RPackage):
+    """This package implements five methods proposed by Resnik, Schlicker,
+    Jiang, Lin and Wang respectively for measuring semantic similarities
+    among DO terms and gene products. Enrichment analyses including
+    hypergeometric model and gene set enrichment analysis are also
+    implemented for discovering disease associations of high-throughput
+    biological data."""
+
+    homepage = "https://www.bioconductor.org/packages/DOSE/"
+    url      = "https://git.bioconductor.org/packages/DOSE"
+
+    version('3.2.0', git='https://git.bioconductor.org/packages/DOSE', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.2.0')
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-gosemsim', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-fgsea', type=('build', 'run'))
+    depends_on('r-do-db', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))