# 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)

import os

from spack import *


class SspaceLongread(Package):
    """SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled
       contigs using long reads

       Note: A manual download is required for SSPACE-LongRead.
       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-longread"
    manual_download = True

    version('1.1', '0bb5d8603d7ead4ff1596135a520cc26')

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

    def url_for_version(self, version):
        return "file://{0}/40SSPACE-LongRead_v{1}.tar.gz".format(
            os.getcwd(), version.dashed)

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install('blasr', prefix.bin)
        install('SSPACE-LongRead.pl', prefix.bin)
