43 lines
2.0 KiB
Python
43 lines
2.0 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class REnsembldb(RPackage):
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"""The package provides functions to create and use transcript centric
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annotation databases/packages. The annotation for the databases are
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directly fetched from Ensembl using their Perl API. The functionality
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and data is similar to that of the TxDb packages from the
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GenomicFeatures package, but, in addition to retrieve all
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gene/transcript models and annotations from the database, the ensembldb
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package provides also a filter framework allowing to retrieve
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annotations for specific entries like genes encoded on a chromosome
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region or transcript models of lincRNA genes."""
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homepage = "https://bioconductor.org/packages/ensembldb/"
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git = "https://git.bioconductor.org/packages/ensembldb.git"
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version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
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depends_on('r-biocgenerics', type=('build', 'run'))
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depends_on('r-genomicranges', type=('build', 'run'))
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depends_on('r-genomicfeatures', type=('build', 'run'))
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depends_on('r-annotationfilter', type=('build', 'run'))
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depends_on('r-rsqlite', type=('build', 'run'))
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depends_on('r-dbi', type=('build', 'run'))
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depends_on('r-biobase', type=('build', 'run'))
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depends_on('r-genomeinfodb', type=('build', 'run'))
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depends_on('r-annotationdbi', type=('build', 'run'))
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depends_on('r-rtracklayer', type=('build', 'run'))
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depends_on('r-s4vectors', type=('build', 'run'))
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depends_on('r-annotationhub', type=('build', 'run'))
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depends_on('r-rsamtools', type=('build', 'run'))
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depends_on('r-iranges', type=('build', 'run'))
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depends_on('r-protgenerics', type=('build', 'run'))
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depends_on('r-biostrings', type=('build', 'run'))
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depends_on('r-curl', type=('build', 'run'))
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depends_on('r@3.4.0:3.4.9', type=('build', 'run'))
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