From 176b518d4b9e91c6b4c05f2fd6242945456a847a Mon Sep 17 00:00:00 2001
From: David Orman <orman@iastate.edu>
Date: Fri, 15 Dec 2017 13:00:55 -0600
Subject: [PATCH] new package: gatk (#6674)

---
 var/spack/repos/builtin/packages/gatk/gatk.sh |  4 +
 .../repos/builtin/packages/gatk/package.py    | 87 +++++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/gatk/gatk.sh
 create mode 100644 var/spack/repos/builtin/packages/gatk/package.py

diff --git a/var/spack/repos/builtin/packages/gatk/gatk.sh b/var/spack/repos/builtin/packages/gatk/gatk.sh
new file mode 100755
index 0000000000..2bd68247a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/gatk.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the gatk jar file
+java -jar GenomeAnalysisTK.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
new file mode 100644
index 0000000000..728fae94da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/package.py
@@ -0,0 +1,87 @@
+##############################################################################
+# 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
+##############################################################################
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install gatk
+#
+# You can edit this file again by typing:
+#
+#     spack edit gatk
+#
+# See the Spack documentation for more information on packaging.
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+from spack import *
+from shutil import copyfile
+import glob
+import os.path
+import re
+
+
+class Gatk(Package):
+    """Genome Analysis Toolkit
+       Variant Discovery in High-Throughput Sequencing Data
+    """
+    homepage = "http://broadinstitute.github.io/gatk/"
+    url      = "https://software.broadinstitute.org/gatk/download/auth?package=GATK"
+    _urlfmt  = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz"
+
+    version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
+            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
+
+    depends_on('java@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        # The list of files to install varies with release...
+        # ... but skip the spack-{build.env}.out files.
+        files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
+        for f in files:
+            install(f, 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__), "gatk.sh")
+        script = join_path(prefix.bin, "gatk")
+        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['java'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('GenomeAnalysisTK.jar', join_path(prefix.bin,
+                    'GenomeAnalysisTK.jar'),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('GATK',
+                             join_path(self.prefix, 'bin',
+                                                    'GenomeAnalysisTK.jar'))