r-biomart: created new package (#5554)

var/spack/repos/builtin/packages/r-biomart/package.py

@@ -0,0 +1,49 @@
+##############################################################################
+# 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 RBiomart(RPackage):
+    """In recent years a wealth of biological data has become available in
+       public data repositories. Easy access to these valuable data resources
+       and firm integration with data analysis is needed for comprehensive
+       bioinformatics data analysis. biomaRt provides an interface to a growing
+       collection of databases implementing the BioMart software suite
+       (http://www.biomart.org). The package enables retrieval of large amounts
+       of data in a uniform way without the need to know the underlying
+       database schemas or write complex SQL queries. Examples of BioMart
+       databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and
+       dbSNP mapped to Ensembl. These major databases give biomaRt users direct
+       access to a diverse set of data and enable a wide range of powerful
+       online queries from gene annotation to database mining."""
+
+    homepage = "https://bioconductor.org/packages/biomaRt/"
+    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/biomaRt_2.32.1.tar.gz"
+
+    version('2.32.1', '9c7f4547dbf4582fc88ca0c65f789328')
+
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))