r-genomicranges: added new package (#5697)

1 files changed, 52 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
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+++ b/var/spack/repos/builtin/packages/r-genomicranges/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 RGenomicranges(RPackage):
+    """The ability to efficiently represent and manipulate genomic annotations
+       and alignments is playing a central role when it comes to analyzing
+       high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges
+       package defines general purpose containers for storing and manipulating
+       genomic intervals and variables defined along a genome. More specialized
+       containers for representing and manipulating short alignments against a
+       reference genome, or a matrix-like summarization of an experiment, are
+       defined in the GenomicAlignments and SummarizedExperiment packages
+       respectively. Both packages build on top of the GenomicRanges
+       infrastructure."""
+
+    homepage = "https://bioconductor.org/packages/GenomicRanges/"
+    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.5.tar.gz"
+    list_url = homepage
+
+    version('1.28.6', '84c5a40e846b35e98d019ca39783cfe6')
+    version('1.28.5', '5b11897331c4371e09133ea3be125c03')
+
+    depends_on('r-biocgenerics', 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-xvector', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.5:1.28.6')