# Copyright 2013-2019 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 import *
import os.path


class Qorts(RPackage):
    """The QoRTs software package is a fast, efficient, and portable
    multifunction toolkit designed to assist in the analysis, quality
    control, and data management of RNA-Seq and DNA-Seq datasets. Its
    primary function is to aid in the detection and identification of
    errors, biases, and artifacts produced by high-throughput sequencing
    technology."""

    homepage = "https://github.com/hartleys/QoRTs"
    url      = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"

    version('1.2.42', sha256='c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08')

    depends_on('java', type='run')

    resource(
        name='QoRTs.jar',
        url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
        sha256='e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce',
        placement='jarfile',
        expand=False
    )

    @run_after('install')
    def install_jar(self):
        install_tree(join_path(self.stage.source_path, 'jarfile'),
                     self.prefix.bin)

        # Set up a helper script to call java on the jar file,
        # explicitly codes the path for java and the jar file.
        script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
        script = self.prefix.bin.QoRTs
        install(script_sh, script)
        set_executable(script)

        # Munge the helper script to explicitly point to java and the
        # jar file.
        java = self.spec['java'].prefix.bin.java
        kwargs = {'backup': False}
        filter_file('^java', java, script, **kwargs)
        filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
                    script, **kwargs)
