# Copyright 2013-2018 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
import glob


class SspaceStandard(Package):
    """SSPACE standard is a stand-alone program for scaffolding pre-assembled
       contigs using NGS paired-read data

       Note: A manual download is required for SSPACE-Standard.
       Spack will search your current directory for the download file.
       Alternatively, add this file to a mirror so that Spack can find it.
       For instructions on how to set up a mirror, see
       http://spack.readthedocs.io/en/latest/mirrors.html"""

    homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
    url      = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())

    version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')

    depends_on('perl+threads', type=('build', 'run'))
    depends_on('perl-perl4-corelibs', type=('build', 'run'))

    def install(self, spec, prefix):
        rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)

        scripts = [rootscript]
        scripts.extend(glob.glob('tools/*.pl'))
        scripts.extend(glob.glob('bwa/*.pl'))

        for s in scripts:
            filter_file('/usr/bin/perl', '/usr/bin/env perl',
                        s, string=True)
            filter_file('require "getopts.pl";', 'use Getopt::Std;',
                        s, string=True)
            filter_file('&Getopts(', 'getopts(', s, string=True)

        install_tree('bin', prefix.bin)
        install_tree('bowtie', prefix.bowtie)
        install_tree('bwa', prefix.bwa)
        install_tree('dotlib', prefix.dotlib)
        install_tree('tools', prefix.tools)
        install(rootscript, prefix)

    def setup_environment(self, spack_env, run_env):
        run_env.set('SSPACE_HOME', prefix)
        run_env.prepend_path('PATH', prefix)