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| -rw-r--r-- | var/spack/repos/builtin/packages/grnboost/package.py | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/grnboost/package.py b/var/spack/repos/builtin/packages/grnboost/package.py new file mode 100644 index 0000000000..b1aedc05ba --- /dev/null +++ b/var/spack/repos/builtin/packages/grnboost/package.py @@ -0,0 +1,61 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/spack/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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) |