a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
43 lines
1.7 KiB
Python
43 lines
1.7 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Grnboost(Package):
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"""GRNBoost is a library built on top of Apache Spark that implements a
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scalable strategy for gene regulatory network (GRN) inference.
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See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md
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for the user guide. The location of xgboost4j-<version>.jar and
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GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to
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xgboost4j-<version>.jar is also added to CLASSPATH."""
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homepage = "https://github.com/aertslab/GRNBoost"
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version('2017-10-9', git='https://github.com/aertslab/GRNBoost.git',
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commit='26c836b3dcbb85852d3c6f4b8340e8655434da02')
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depends_on('sbt', type='build')
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depends_on('java', type=('build', 'run'))
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depends_on('xgboost+jvm-packages', type='run')
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depends_on('spark+hadoop', type='run')
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def setup_run_environment(self, env):
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grnboost_jar = join_path(self.prefix, 'target',
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'scala-2.11', 'GRNBoost.jar')
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xgboost_version = self.spec['xgboost'].version.string
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xgboost_jar = join_path(self.spec['xgboost'].prefix,
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'xgboost4j-' + xgboost_version + '.jar')
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env.set('GRNBOOST_JAR', grnboost_jar)
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env.set('JAVA_HOME', self.spec['java'].prefix)
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env.set('CLASSPATH', xgboost_jar)
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env.set('XGBOOST_JAR', xgboost_jar)
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def install(self, spec, prefix):
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sbt = which('sbt')
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sbt('assembly')
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install_tree('target', prefix.target)
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