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# Copyright 2013-2023 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 REnsembldb(RPackage):
"""Utilities to create and use Ensembl-based annotation databases.
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, ensembldb
provides a filter framework allowing to retrieve annotations for
specific entries like genes encoded on a chromosome region or transcript
models of lincRNA genes. EnsDb databases built with ensembldb contain
also protein annotations and mappings between proteins and their
encoding transcripts. Finally, ensembldb provides functions to map
between genomic, transcript and protein coordinates."""
bioc = "ensembldb"
version("2.24.0", commit="45a79a438fde11b0d244b071e6ae2b652100be03")
version("2.22.0", commit="4dda178a14e080c643bbd8c4dd6378bfe4e6ee9f")
version("2.20.2", commit="ac1fb8389efd88099600af298d6bb3384206f9ed")
version("2.20.1", commit="e547d184730cfe5e65f59e4f3512395fb1cdba1a")
version("2.18.3", commit="e2fcfc0c7700110df070a171d2d542b37ec098f3")
version("2.14.0", commit="c7150519ed4ef38e5eac1043209863dbc7be43a1")
version("2.8.1", commit="a4d8d89c143dca86b364d59dff8e46cc81c41ac0")
version("2.6.8", commit="c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c")
version("2.4.1", commit="b5b6b94826a2f46a4faecb9dde750ecd3bfaf327")
version("2.2.2", commit="d71610e58aed88dbbe6a74e7a8ddfb7451398060")
version("2.0.4", commit="514623d71e3cca7a4e547adb579b5a958702ef86")
depends_on("r@3.5.0:", type=("build", "run"), when="@2.20.1:")
depends_on("r-biocgenerics@0.15.10:", type=("build", "run"))
depends_on("r-genomicranges@1.23.21:", type=("build", "run"))
depends_on("r-genomicranges@1.31.18:", type=("build", "run"), when="@2.4.1:")
depends_on("r-genomicfeatures@1.23.18:", type=("build", "run"))
depends_on("r-genomicfeatures@1.29.10:", type=("build", "run"), when="@2.2.2:")
depends_on("r-genomicfeatures@1.49.6:", type=("build", "run"), when="@2.22.0:")
depends_on("r-annotationfilter@0.99.7:", type=("build", "run"))
depends_on("r-annotationfilter@1.1.9:", type=("build", "run"), when="@2.2.2:")
depends_on("r-annotationfilter@1.5.2:", type=("build", "run"), when="@2.6.8:")
depends_on("r-rsqlite@1.1:", 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@1.31.19:", type=("build", "run"))
depends_on("r-rtracklayer", type=("build", "run"))
depends_on("r-s4vectors", type=("build", "run"))
depends_on("r-s4vectors@0.23.10:", type=("build", "run"), when="@2.14.0:")
depends_on("r-rsamtools", type=("build", "run"))
depends_on("r-iranges", type=("build", "run"))
depends_on("r-iranges@2.11.16:", type=("build", "run"), when="@2.2.2:")
depends_on("r-iranges@2.13.24:", type=("build", "run"), when="@2.4.1:")
depends_on("r-protgenerics", type=("build", "run"))
depends_on("r-biostrings", type=("build", "run"))
depends_on("r-biostrings@2.47.9:", type=("build", "run"), when="@2.4.1:")
depends_on("r-curl", type=("build", "run"))
depends_on("r-annotationhub", type=("build", "run"), when="@2.0.4:2.2.2")
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