varscan: new package (#5026)

* varscan: new package

* changing jdk to java

var/spack/repos/builtin/packages/varscan/package.py

@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/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 *
+import os.path
+
+
+class Varscan(Package):
+    """Variant calling and somatic mutation/CNV detection for next-generation
+       sequencing data"""
+
+    homepage = "http://dkoboldt.github.io/varscan/"
+    url      = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
+
+    version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False)
+
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.jar)
+        jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted)
+        install(jar_file, prefix.jar)
+
+        script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
+        script = prefix.bin.varscan
+        install(script_sh, script)
+        set_executable(script)
+
+        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('varscan.jar', join_path(prefix.jar, jar_file),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('VARSCAN_HOME', self.prefix)
+        run_env.set('CLASSPATH', self.prefix.jar)

var/spack/repos/builtin/packages/varscan/varscan.sh

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+#!/bin/sh
+# convenience wrapper for the astral jar file
+java $JAVA_ARGS $JAVA_OPTS -jar varscan.jar "$@"