r-somaticsignatures: created new package (#6065)

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
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+++ b/var/spack/repos/builtin/packages/r-somaticsignatures/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 RSomaticsignatures(RPackage):
+    """The SomaticSignatures package identifies mutational signatures of
+       single nucleotide variants (SNVs). It provides a infrastructure related
+       to the methodology described in Nik-Zainal (2012, Cell), with
+       flexibility in the matrix decomposition algorithms."""
+
+    homepage = "https://bioconductor.org/packages/SomaticSignatures/"
+    url      = "https://git.bioconductor.org/packages/SomaticSignatures"
+    list_url = homepage
+
+    version('2.12.1', git='https://git.bioconductor.org/packages/SomaticSignatures', commit='932298c6877d076004de5541cec85a14e819517a')
+
+    depends_on('r-variantannotation', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-ggbio', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-pcamethods', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-proxy', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.12.1')