# 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
import glob


class Gapfiller(Package):
    """GapFiller is a stand-alone program for closing gaps within
       pre-assembled scaffolds.

       Note: A manual download is required for GapFiller.
       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/gapfiller"

    version('1.10', '54d5e2ada131a1305a66e41c0d380382')

    def url_for_version(self, version):
        return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
                os.getcwd(), version.dashed)

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

    def patch(self):
        with working_dir('.'):
            files = glob.iglob("*.pl")
            for file in files:
                change = FileFilter(file)
                change.filter('usr/bin/perl', 'usr/bin/env perl')
                change.filter('require "getopts.pl";', 'use Getopt::Std;')
                change.filter('&Getopts', 'getopts')
                change.filter('\r', '')
                set_executable(file)

    def install(self, spec, prefix):
        install_tree('bowtie', prefix.bin.bowtie)
        install_tree('bwa', prefix.bin.bwa)
        install('GapFiller.pl', prefix.bin)
