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# 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)
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