From 11e064d7d1b5b67f876240e4bc1433a3a6640540 Mon Sep 17 00:00:00 2001
From: Eric <erimar77@users.noreply.github.com>
Date: Thu, 15 Feb 2018 18:23:59 -0600
Subject: [PATCH] new package: pilon (#7033)

---
 .../repos/builtin/packages/pilon/package.py   | 60 +++++++++++++++++++
 .../repos/builtin/packages/pilon/pilon.sh     |  3 +
 2 files changed, 63 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/pilon/package.py
 create mode 100644 var/spack/repos/builtin/packages/pilon/pilon.sh

diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py
new file mode 100644
index 0000000000..a075ce9fd8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/package.py
@@ -0,0 +1,60 @@
+##############################################################################
+# 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 Pilon(Package):
+    """Pilon is an automated genome assembly improvement and variant
+    detection tool."""
+
+    homepage = "https://github.com/broadinstitute/pilon"
+    url      = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
+
+    version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
+    version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
+
+    depends_on('java@1.7:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'pilon-{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__), "pilon.sh")
+        script = join_path(prefix.bin, "pilon")
+        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('pilon-{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/pilon/pilon.sh b/var/spack/repos/builtin/packages/pilon/pilon.sh
new file mode 100644
index 0000000000..41a31b3407
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/pilon.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the pilon jar file
+java -jar pilon.jar "$@"