r-ensembldb: created new package (#6038)

1 files changed, 62 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
new file mode 100644
index 0000000000..0439f60019
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+++ b/var/spack/repos/builtin/packages/r-ensembldb/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 REnsembldb(RPackage):
+    """The package provides functions to create and use transcript centric
+       annotation databases/packages. The annotation for the databases are
+       directly fetched from Ensembl using their Perl API. The functionality
+       and data is similar to that of the TxDb packages from the
+       GenomicFeatures package, but, in addition to retrieve all
+       gene/transcript models and annotations from the database, the ensembldb
+       package provides also a filter framework allowing to retrieve
+       annotations for specific entries like genes encoded on a chromosome
+       region or transcript models of lincRNA genes."""
+
+    homepage = "https://bioconductor.org/packages/ensembldb/"
+    url      = "https://git.bioconductor.org/packages/ensembldb"
+    list_url = homepage
+
+    version('2.0.4', git='https://git.bioconductor.org/packages/ensembldb', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicfeatures', type=('build', 'run'))
+    depends_on('r-annotationfilter', type=('build', 'run'))
+    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-annotationhub', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-protgenerics', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-curl', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', type=('build', 'run'))