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# Copyright 2013-2022 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.package import *
class RGenomicfeatures(RPackage):
"""Conveniently import and query gene models.
A set of tools and methods for making and manipulating transcript
centric annotations. With these tools the user can easily download the
genomic locations of the transcripts, exons and cds of a given organism,
from either the UCSC Genome Browser or a BioMart database (more sources
will be supported in the future). This information is then stored in a
local database that keeps track of the relationship between transcripts,
exons, cds and genes. Flexible methods are provided for extracting the
desired features in a convenient format."""
bioc = "GenomicFeatures"
version('1.48.3', commit='b0ddea0e101e3861928f3ad353348df047d90382')
version('1.46.4', commit='d3ab6fd069624904ce7fcdf75dad884473f97975')
version('1.42.1', commit='2e82891974138b0e976799d64a8938f0be61284d')
version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555')
version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387')
version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1')
version('1.30.3', commit='496bbf81beebd7c934b8d3dcea001e3e4a7d7dee')
version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.48.3:')
depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.29:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-iranges@2.9.19:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.30.3:')
depends_on('r-iranges@2.13.23:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.30.3:')
depends_on('r-genomeinfodb@1.15.4:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-genomeinfodb@1.25.7:', type=('build', 'run'), when='@1.42.1:')
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.30.3:')
depends_on('r-genomicranges@1.31.17:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-annotationdbi@1.33.15:', type=('build', 'run'))
depends_on('r-annotationdbi@1.41.4:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite@2.0:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-biostrings@2.23.3:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-biocio', type=('build', 'run'), when='@1.46.4:')
depends_on('r-rtracklayer@1.29.24:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-rtracklayer@1.51.5:', type=('build', 'run'), when='@1.46.4:')
depends_on('r-biomart@2.17.1:', type=('build', 'run'))
depends_on('r-biobase@2.15.1:', type=('build', 'run'))
depends_on('r-rmysql', type=('build', 'run'), when='@1.30.3')
|
