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# Copyright 2013-2023 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.package 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"
license("BSD-3-Clause")
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", 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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