r-genomeinfodb: created new package (#5695)

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
new file mode 100644
index 0000000000..6d3dbe7349
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 RGenomeinfodb(RPackage):
+    """Contains data and functions that define and allow translation between
+       different chromosome sequence naming conventions (e.g., "chr1"
+       versus "1"), including a function that attempts to place sequence
+       names in their natural, rather than lexicographic, order."""
+
+    homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
+    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomeInfoDb_1.12.2.tar.gz"
+    list_url = homepage
+
+    version('1.12.3', '035e120026904df964a79617a8b3e6c6')
+    version('1.12.2', '55b5399d9c8c58b093dfa5f69f8ce2cc')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-genomeinfodbdata', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.12.3')