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# Copyright 2013-2024 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 BioconductorTximeta(RPackage):
"""Transcript Quantification Import with Automatic Metadata
Transcript quantification import from Salmon and alevin with automatic
attachment of transcript ranges and release information, and other associated
metadata. De novo transcriptomes can be linked to the appropriate sources with
linkedTxomes and shared for computational reproducibility."""
homepage = "https://bioconductor.org/packages/release/bioc/html/tximeta.html"
url = "https://bioconductor.org/packages/release/bioc/src/contrib/tximeta_1.18.1.tar.gz"
bioc = "tximeta"
version(
"1.18.1",
sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408",
deprecated=True,
)
depends_on("r", type=("build", "run"))
depends_on("r-annotationdbi")
depends_on("r-annotationhub")
depends_on("r-biocfilecache")
depends_on("r-biostrings")
depends_on("r-ensembldb")
depends_on("r-genomeinfodb")
depends_on("r-genomicfeatures")
depends_on("r-genomicranges")
depends_on("r-iranges")
depends_on("r-s4vectors")
depends_on("r-summarizedexperiment")
depends_on("r-tximport")
depends_on("r-jsonlite")
depends_on("r-matrix")
depends_on("r-tibble")
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