# Copyright 2013-2021 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 Grnboost(Package):
    """GRNBoost is a library built on top of Apache Spark that implements a
    scalable strategy for gene regulatory network (GRN) inference.

    See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md
    for the user guide. The location of xgboost4j-<version>.jar and
    GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to
    xgboost4j-<version>.jar is also added to CLASSPATH."""

    homepage = "https://github.com/aertslab/GRNBoost"

    version('2017-10-9', git='https://github.com/aertslab/GRNBoost.git',
            commit='26c836b3dcbb85852d3c6f4b8340e8655434da02')

    depends_on('sbt', type='build')
    depends_on('java', type=('build', 'run'))
    depends_on('xgboost+jvm-packages', type='run')
    depends_on('spark+hadoop', type='run')

    def setup_run_environment(self, env):
        grnboost_jar = join_path(self.prefix, 'target',
                                 'scala-2.11', 'GRNBoost.jar')
        xgboost_version = self.spec['xgboost'].version.string
        xgboost_jar = join_path(self.spec['xgboost'].prefix,
                                'xgboost4j-' + xgboost_version + '.jar')
        env.set('GRNBOOST_JAR', grnboost_jar)
        env.set('JAVA_HOME', self.spec['java'].prefix)
        env.set('CLASSPATH', xgboost_jar)
        env.set('XGBOOST_JAR', xgboost_jar)

    def install(self, spec, prefix):
        sbt = which('sbt')
        sbt('assembly')
        install_tree('target', prefix.target)