r-acde: Create new package. (#5616)

var/spack/repos/builtin/packages/r-acde/package.py

@@ -0,0 +1,46 @@
+##############################################################################
+# 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 RAcde(RPackage):
+    """This package provides a multivariate inferential analysis method
+    for detecting differentially expressed genes in gene expression data.
+    It uses artificial components, close to the data's principal
+    components but with an exact interpretation in terms of differential
+    genetic expression, to identify differentially expressed genes while
+    controlling the false discovery rate (FDR). The methods on this
+    package are described in the vignette or in the article
+    'Multivariate Method for Inferential Identification of
+    Differentially Expressed Genes in Gene Expression Experiments' by
+    J. P. Acosta, L. Lopez-Kleine and S. Restrepo
+    (2015, pending publication)."""
+
+    homepage = "https://www.bioconductor.org/packages/acde/"
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/acde_1.6.0.tar.gz"
+
+    version('1.6.0', 'e92ce91f75bab3bb1d79995bec1b42cc')
+
+    depends_on('r-boot', type=('build', 'run'))