# 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 Bismark(Package):
    """A tool to map bisulfite converted sequence reads and determine cytosine
    methylation states"""

    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
    url      = "https://github.com/FelixKrueger/Bismark/archive/0.23.0.tar.gz"

    version('0.23.0', sha256='ea1625808487c1442dbf825d9cbe5c0cbc37ea5bd1460f59e1e0ccc80cc01c9e')
    version('0.19.0', sha256='91707737f96a0574956a282b635abad7560e7d90bee188a67a7807b2470deae2')
    version('0.18.2', sha256='83391c5b5af33047178e7774ac25f5a69ce9315c13ae02f016baf7c50b73e702')

    depends_on('bowtie2', type='run')
    depends_on('perl', type='run')
    depends_on('samtools', type='run')

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install('bam2nuc', prefix.bin)
        install('bismark', prefix.bin)
        install('bismark_genome_preparation', prefix.bin)
        install('bismark_methylation_extractor', prefix.bin)
        install('bismark2bedGraph', prefix.bin)
        install('bismark2report', prefix.bin)
        install('bismark2summary', prefix.bin)
        install('coverage2cytosine', prefix.bin)
        install('deduplicate_bismark', prefix.bin)
        install('filter_non_conversion', prefix.bin)
        install('NOMe_filtering', prefix.bin)
