# 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 PyPipits(PythonPackage):
    """Automated pipeline for analyses of fungal ITS from the Illumina"""

    homepage = "https://github.com/hsgweon/pipits"
    url      = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz"

    version('2.4', sha256='b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054')
    version('1.5.0', sha256='6c76fff42a9db62ff4bb1d4d520ebee6cb20d5a726f12c3d5a3d42314947a659')

    # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml
    depends_on('python@3:', type=('build', 'run'), when='@2:')
    depends_on('python@:2', type=('build', 'run'), when='@:1')
    depends_on('py-setuptools', type='build', when='@2:')
    depends_on('py-pispino@1.1:', type=('build', 'run'), when='@2:')
    depends_on('vsearch', type='run')
    depends_on('fastx-toolkit', type='run')
    depends_on('hmmer', type='run')
    depends_on('itsx', type='run')
    depends_on('py-biom-format', type=('build', 'run'))
    depends_on('rdptools', type='run', when='@2:')
    depends_on('py-numpy', type=('build', 'run'))
    depends_on('py-pandas', type=('build', 'run'), when='@2:')
    depends_on('py-progressbar2', type=('build', 'run'), when='@2:')
    depends_on('py-requests', type=('build', 'run'), when='@2:')
    depends_on('seqkit', type='run')
    depends_on('java', type=('build', 'run'), when='@:1')
    depends_on('rdp-classifier', type='run', when='@:1')

    resource(
        name='UNITE_retrained',
        url='http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz',
        destination='refdb'
    )

    resource(
        name='uchime_reference_dataset_01.01.2016.fasta',
        url='https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip',
        destination=join_path('refdb', 'uchime_reference_dataset_01.01.2016')
    )

    resource(
        name='warcup_retrained_V2',
        url='https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz',
        destination='refdb'
    )

    @run_after('install')
    def install_db(self):
        install_tree(join_path(self.stage.source_path, 'refdb'),
                     self.prefix.refdb)

    def setup_run_environment(self, env):
        env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path(
                self.prefix, 'refdb',
                'uchime_reference_dataset_01.01.2016',
                'uchime_reference_dataset_01.01.2016.fasta'))
        env.set('PIPITS_UNITE_RETRAINED_DIR',
                self.prefix.refdb.UNITE_retrained)
        env.set('PIPITS_WARCUP_RETRAINED_DIR',
                self.prefix.refdb.warcup_retrained_V2)
        env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path(
                self.spec['rdp-classifier'].prefix.bin,
                'classifier.jar'))