# Copyright 2013-2020 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 glob


class Redundans(Package):
    """Redundans pipeline assists an assembly of heterozygous genomes."""

    homepage = "https://github.com/Gabaldonlab/redundans"
    url      = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
    git      = "https://github.com/Gabaldonlab/redundans.git"

    version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0')
    version('0.13c', sha256='26d48f27a32678d94c1d00cb3b8991d74891d6cad64a94569901ff9607a7a736')

    depends_on('python', type=('build', 'run'))
    depends_on('py-pyscaf', type=('build', 'run'))
    depends_on('py-fastaindex', type=('build', 'run'))
    depends_on('py-numpy', type=('build', 'run'))
    depends_on('perl', type=('build', 'run'))
    depends_on('sspace-standard')
    depends_on('bwa')
    depends_on('last')
    depends_on('gapcloser')
    depends_on('parallel')
    depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))

    def install(self, spec, prefix):
        sspace_location = join_path(spec['sspace-standard'].prefix,
                                    'SSPACE_Standard_v3.0.pl')

        filter_file(r'sspacebin = os.path.join(.*)$',
                    'sspacebin = \'' + sspace_location + '\'',
                    'redundans.py')

        binfiles = ['redundans.py', 'bin/filterReads.py']
        binfiles.extend(glob.glob('bin/fast?2*.py'))

        # new internal dep with 0.14a
        if spec.satisfies('@0.14a:'):
            binfiles.append('bin/denovo.py')

        mkdirp(prefix.bin)
        for f in binfiles:
            install(f, prefix.bin)