# 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)