##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os


class Trf(Package):
    """Tandem Repeats Finder is a program to locate and display tandem repeats
       in DNA sequences.

       Note: A manual download is required for TRF.
       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://tandem.bu.edu/trf/trf.html"

    version('4.09', '0c594fe666e0332db1df9d160d7fabc8', expand=False,
            url='file://{0}/trf409.linux64'.format(os.getcwd()))

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install('trf409.linux64', prefix.bin.trf)
        chmod = which('chmod')
        chmod('+x', prefix.bin.trf)