RNA-SeQC: Create new package (#6555)

* RNA-SeQC: Create new package

* RNA-SeQC: Fix flake8 error

* RNA-SeQC: Fix Travis error

var/spack/repos/builtin/packages/rna-seqc/package.py

@@ -0,0 +1,63 @@
+##############################################################################
+# 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 *
+from shutil import copyfile
+import os.path
+
+
+class RnaSeqc(Package):
+    """RNA-SeQC is a java program which computes a series of quality control
+    metrics for RNA-seq data."""
+
+    homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
+    url      = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
+
+    version('1.1.8', '71d7b5d3b3dcc1893cdc7f6819185d41', expand=False)
+    version('1.1.7', '2d0b8ecac955af2f9bc1b185fdfb6b45', expand=False)
+    version('1.1.6', 'fa9c9885081ae2e47f285c7c0f596a14', expand=False)
+    version('1.1.5', '4b875671e906f708cbb8fd9bcf0e958d', expand=False)
+    version('1.1.4', 'b04d06947c48cb2dc1b0ba29c8232db5', expand=False)
+
+    depends_on('jdk@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted)
+        install(jar_file, 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__), "rna-seqc.sh")
+        script = join_path(prefix.bin, "rna-seqc")
+        copyfile(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = join_path(self.spec['jdk'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)

var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh

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+#!/bin/sh
+# convenience wrapper for the rna-seqc jar file
+java -jar RNA-SeQC_v{}.jar "$@"