New package: GRNBoost (#8763)

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)