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+# Copyright 2013-2018 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_environment(self, spack_env, run_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')
+ run_env.set('GRNBOOST_JAR', grnboost_jar)
+ run_env.set('JAVA_HOME', self.spec['java'].prefix)
+ run_env.set('CLASSPATH', xgboost_jar)
+ run_env.set('XGBOOST_JAR', xgboost_jar)
+
+ def install(self, spec, prefix):
+ sbt = which('sbt')
+ sbt('assembly')
+ install_tree('target', prefix.target)