##############################################################################
# Copyright (c) 2013-2016, 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/llnl/spack
# Please also see the LICENSE file 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 *
from distutils.dir_util import copy_tree, mkpath
from distutils.file_util import copy_file


class Fastqc(Package):
    """A quality control tool for high throughput sequence data."""

    homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
    url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"

    version('0.11.5', '3524f101c0ab0bae77c7595983170a76')

    depends_on('jdk', type='run')
    depends_on('perl')          # for fastqc "script", any perl will do

    patch('fastqc.patch', level=0)

    def install(self, spec, prefix):
        mkpath(self.prefix.bin)
        mkpath(self.prefix.lib)
        copy_file('fastqc', self.prefix.bin)
        for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
            copy_file(j, self.prefix.lib)
        for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
            copy_tree(d, join_path(self.prefix.lib, d))
        chmod = which('chmod')
        chmod('+x', join_path(self.prefix.bin, 'fastqc'))

    # In theory the 'run' dependency on 'jdk' above should take
    # care of this for me. In practice, it does not.
    def setup_environment(self, spack_env, run_env):
        """Add <prefix> to the path; the package has a script at the
           top level.
        """
        run_env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin'))