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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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/"
git = "https://git.bioconductor.org/packages/ensembldb.git"
version('2.0.4', 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'))
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