r-mergemaid: created new package (#6182)

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/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 RMergemaid(RPackage):
+    """The functions in this R extension are intended for cross-study
+       comparison of gene expression array data. Required from the user is
+       gene expression matrices, their corresponding gene-id vectors and
+       other useful information, and they could be 'list','matrix', or
+       'ExpressionSet'. The main function is 'mergeExprs' which transforms
+       the input objects into data in the merged format, such that common
+       genes in different datasets can be easily found. And the function
+       'intcor' calculate the correlation coefficients. Other functions use
+       the output from 'modelOutcome' to graphically display the results and
+       cross-validate associations of gene expression data with survival."""
+
+    homepage = "https://www.bioconductor.org/packages/MergeMaid/"
+    url      = "https://git.bioconductor.org/packages/MergeMaid"
+
+    version('2.48.0', git='https://git.bioconductor.org/packages/MergeMaid', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
+
+    depends_on('r-survival', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.48.0')