# Copyright 2013-2018 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 Mefit(Package):
    """This pipeline will merge overlapping paired-end reads, calculate
    merge statistics, and filter reads for quality."""

    homepage = "https://github.com/nisheth/MeFiT"
    git      = "https://github.com/nisheth/MeFiT.git"

    version('1.0', commit='0733326d8917570bbf70ff5c0f710bf66c13db09')

    depends_on('py-numpy')
    depends_on('py-htseq')
    depends_on('jellyfish')
    depends_on('casper %gcc@4.8.5')

    def install(self, spec, prefix):
        install_tree('.', prefix)

    def setup_environment(self, spack_env, run_env):
        run_env.prepend_path('PATH', self.prefix)
