# 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 Tabix(MakefilePackage):
    """Generic indexer for TAB-delimited genome position files"""

    homepage = "https://github.com/samtools/tabix"
    git      = "https://github.com/samtools/tabix.git"

    version('2013-12-16', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')

    depends_on('perl', type=('build', 'run'))
    depends_on('python', type=('build', 'run'))
    depends_on('zlib', type='link')

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        mkdirp(prefix.share.man.man1)
        install('tabix', prefix.bin)
        install('bgzip', prefix.bin)
        install('tabix.py', prefix.bin)
        install('tabix.1', prefix.share.man.man1)
        install('tabix.tex', prefix.share)
        install('TabixReader.java', prefix.bin)
        install('libtabix.a', prefix.lib)
        install_tree('perl', prefix.perl)
        install_tree('python', prefix.python)