1 files changed, 40 insertions, 0 deletions
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..afcdfd4a44
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+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 = prefix.bin.pilon
+        install(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 = {'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)