# Copyright 2013-2021 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 *


class Pagit(Package):
    """PAGIT addresses the need for software to generate high quality draft
       genomes."""

    homepage = "https://www.sanger.ac.uk/science/tools/pagit"
    url      = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz"

    version('1.01', sha256='8069c1d236804cf4ea782495adcc50d18561ef466af06b21946b980b3c37ad55')

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

    def install(self, spec, prefix):
        with working_dir('PAGIT'):
            install_tree('ABACAS', prefix.ABACAS)
            install_tree('bin', prefix.bin)
            install_tree('ICORN', prefix.ICORN)
            install_tree('IMAGE', prefix.IMAGE)
            install_tree('lib', prefix.lib)
            install_tree('RATT', prefix.RATT)

    def setup_run_environment(self, env):
        env.set('PAGIT_HOME', self.prefix)
        env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5'))
        env.set('ICORN_HOME', self.prefix.icorn)
        env.set('SNPOMATIC_HOME', self.prefix.bin)
        env.set('RATT_HOME', self.prefix.RATT)
        env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config'))
        env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5',
                         'ssaha2'))
        env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5'))
        env.prepend_path('PATH', self.prefix.IMAGE)
        env.prepend_path('PATH', self.prefix.ABACAS)
        env.prepend_path('PATH', self.prefix.ICORN)
        env.prepend_path('PATH', self.prefix.RATT)
        env.prepend_path('PERL5LIB', self.prefix.lib)