r-minfi: created new package (#5887)

1 files changed, 63 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
new file mode 100644
index 0000000000..f94a87b4f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-minfi/package.py
@@ -0,0 +1,63 @@
+##############################################################################
+# 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 RMinfi(RPackage):
+    """Tools to analyze & visualize Illumina Infinium methylation arrays."""
+
+    homepage = "https://bioconductor.org/packages/minfi/"
+    url      = "https://git.bioconductor.org/packages/minfi"
+    list_url = homepage
+
+    version('1.22.1', git='https://git.bioconductor.org/packages/minfi', commit='b2faf84bcbb291e32d470a0e029450093527545b')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-summarizedexperiment', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-bumphunter', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-beanplot', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-nor1mix', type=('build', 'run'))
+    depends_on('r-siggenes', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-preprocesscore', type=('build', 'run'))
+    depends_on('r-illuminaio', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-genefilter', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-reshape', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-quadprog', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-geoquery', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.22.1')