r-yapsa: created new package (#6121)

1 files changed, 57 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-yapsa/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 RYapsa(RPackage):
+    """This package provides functions and routines useful in the analysis of
+       somatic signatures (cf. L. Alexandrov et al., Nature 2013). In
+       particular, functions to perform a signature analysis with known
+       signatures (LCD = linear combination decomposition) and a signature
+       analysis on stratified mutational catalogue (SMC = stratify mutational
+       catalogue) are provided."""
+
+    homepage = "http://bioconductor.org/packages/YAPSA/"
+    url      = "https://git.bioconductor.org/packages/YAPSA"
+    list_url = homepage
+
+    version('1.2.0', git='https://git.bioconductor.org/packages/YAPSA', commit='320809b69e470e30a777a383f8341f93064ec24d')
+
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-lsei', type=('build', 'run'))
+    depends_on('r-somaticsignatures', type=('build', 'run'))
+    depends_on('r-variantannotation', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-corrplot', type=('build', 'run'))
+    depends_on('r-dendextend', type=('build', 'run'))
+    depends_on('r-getoptlong', type=('build', 'run'))
+    depends_on('r-gtrellis', type=('build', 'run'))
+    depends_on('r-pmcmr', type=('build', 'run'))
+    depends_on('r-complexheatmap', type=('build', 'run'))
+    depends_on('r-keggrest', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.2.0')