a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
61 lines
3.2 KiB
Python
61 lines
3.2 KiB
Python
# Copyright 2013-2021 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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"""Utilities to create and use Ensembl-based annotation databases.
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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, ensembldb
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provides a filter framework allowing to retrieve annotations for
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specific entries like genes encoded on a chromosome region or transcript
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models of lincRNA genes. EnsDb databases built with ensembldb contain
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also protein annotations and mappings between proteins and their
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encoding transcripts. Finally, ensembldb provides functions to map
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between genomic, transcript and protein coordinates."""
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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('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
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version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c')
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version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327')
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version('2.2.2', commit='d71610e58aed88dbbe6a74e7a8ddfb7451398060')
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version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
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depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
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depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
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depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run'))
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depends_on('r-annotationfilter@0.99.7:', type=('build', 'run'))
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depends_on('r-rsqlite@1.1:', 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@1.31.19:', 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', when='@2.0.4:2.2.2', 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-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run'))
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depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run'))
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depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run'))
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depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run'))
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depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run'))
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depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run'))
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depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run'))
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