astral: new package (#5022)

* astral: new package

* simplifying join_path

* adding build phase and changing jdk to java

* forgot to change jdk to java....

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

@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the astral jar file
+java $JAVA_ARGS $JAVA_OPTS -jar astral.jar "$@"

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

@@ -0,0 +1,64 @@
+##############################################################################
+# 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 Astral(Package):
+    """ASTRAL is a tool for estimating an unrooted species tree given a set of
+       unrooted gene trees."""
+
+    homepage = "https://github.com/smirarab/ASTRAL"
+    url      = "https://github.com/smirarab/ASTRAL/archive/v4.10.7.tar.gz"
+
+    version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d')
+
+    depends_on('java', type=('build', 'run'))
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        make = Executable('./make.sh')
+        make()
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('lib', prefix.tools.lib)
+        jar_file = 'astral.{v}.jar'.format(v=self.version)
+        install(jar_file, prefix.tools)
+
+        script_sh = join_path(os.path.dirname(__file__), "astral.sh")
+        script = prefix.bin.astral
+        install(script_sh, script)
+        set_executable(script)
+
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('astral.jar', join_path(prefix.tools, jar_file),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('ASTRAL_HOME', self.prefix.tools)