r-qorts: Create new package. (#8744)

* r-qorts: Create new package.

* Change dependency to java, change package name.

* Remove some join_path.

var/spack/repos/builtin/packages/qorts/QoRTs.sh

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

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

@@ -0,0 +1,71 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 *
+import os.path
+from shutil import copyfile
+
+
+class Qorts(RPackage):
+    """The QoRTs software package is a fast, efficient, and portable
+    multifunction toolkit designed to assist in the analysis, quality
+    control, and data management of RNA-Seq and DNA-Seq datasets. Its
+    primary function is to aid in the detection and identification of
+    errors, biases, and artifacts produced by high-throughput sequencing
+    technology."""
+
+    homepage = "https://github.com/hartleys/QoRTs"
+    url      = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
+
+    version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829')
+
+    depends_on('java', type='run')
+
+    resource(
+        name='QoRTs.jar',
+        url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
+        md5='918df4291538218c12caa3ab98c535e9',
+        placement='jarfile',
+        expand=False
+    )
+
+    @run_after('install')
+    def install_jar(self):
+        install_tree(join_path(self.stage.source_path, 'jarfile'),
+                     self.prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
+        script = self.prefix.bin.QoRTs
+        copyfile(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'backup': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
+                    script, **kwargs)