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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 PerlStarFusion(Package):
"""STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis
Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate
fusion transcripts supported by Illumina reads. STAR-Fusion further
processes the output generated by the STAR aligner to map junction reads
and spanning reads to a reference annotation set."""
homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
git = "https://github.com/STAR-Fusion/STAR-Fusion.git"
license("BSD-3-Clause")
version("master", commit="8c5a541ab701debebb68e5c4ee9d6a03e03d65ca")
extends("perl")
depends_on("star", type=("build", "run"))
depends_on("perl", type=("build", "run"))
depends_on("perl-set-intervaltree", type=("build", "run"))
depends_on("perl-dbi", type=("build", "run"))
depends_on("perl-db-file", type=("build", "run"))
depends_on("perl-uri", type=("build", "run"))
def install(self, spec, prefix):
mkdirp(perl_lib_dir)
install(join_path("PerlLib", "*.pm"), perl_lib_dir)
install_tree("util", prefix.bin)
install("STAR-Fusion", prefix.bin)
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