r-abaenrichment: Create new package. (#5612)

1 files changed, 52 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/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/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 RAbaenrichment(RPackage):
+    """The package ABAEnrichment is designed to test for enrichment
+    of user defined candidate genes in the set of expressed genes in
+    different human brain regions. The core function 'aba_enrich'
+    integrates the expression of the candidate gene set (averaged
+    across donors) and the structural information of the brain using
+    an ontology, both provided by the Allen Brain Atlas project.
+    'aba_enrich' interfaces the ontology enrichment software FUNC to
+    perform the statistical analyses. Additional functions provided
+    in this package like 'get_expression' and 'plot_expression'
+    facilitate exploring the expression data. From version 1.3.5
+    onwards genomic regions can be provided as input, too; and from
+    version 1.5.9 onwards the function 'get_annotated_genes' offers
+    an easy way to obtain annotations of genes to enriched or
+    user-defined brain regions."""
+
+    homepage = "https://bioconductor.org/packages/ABAEnrichment/"
+    url      = "https://bioconductor.org/packages/release/bioc/src/contrib/ABAEnrichment_1.6.0.tar.gz"
+
+    version('1.6.0', '810eb4ee9ce2a5049babbb174dc8d588')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-gplots', type=('build', 'run'))
+    depends_on('r-gtools', type=('build', 'run'))
+    depends_on('r-abadata', type=('build', 'run'))