# Copyright 2013-2022 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 Tcoffee(MakefilePackage):
    """T-Coffee is a multiple sequence alignment program."""

    homepage = "http://www.tcoffee.org/"
    git      = "https://github.com/cbcrg/tcoffee.git"

    version('2017-08-17', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')

    depends_on('perl', type=('build', 'run'))
    depends_on('blast-plus')
    depends_on('dialign-tx')
    depends_on('viennarna')
    depends_on('clustalw')
    depends_on('tmalign')
    depends_on('muscle')
    depends_on('mafft')
    depends_on('pcma')
    depends_on('poamsa')
    depends_on('probconsrna')

    build_directory = 'compile'

    def build(self, spec, prefix):
        with working_dir(self.build_directory):
            make('t_coffee')

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        with working_dir(self.build_directory):
            install('t_coffee', prefix.bin)