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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 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"
version('master', commit='8c5a541')
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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