1 files changed, 42 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py
new file mode 100644
index 0000000000..81e7147d20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/package.py
@@ -0,0 +1,42 @@
+# 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 Snpeff(Package):
+    """SnpEff is a variant annotation and effect prediction tool. It
+    annotates and predicts the effects of genetic variants (such as
+    amino acid changes)."""
+
+    homepage = "http://snpeff.sourceforge.net/"
+    url      = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
+
+    version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
+
+    depends_on('jdk', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('snpEff', prefix.bin)
+
+        # Set up a helper script to call java on the jar files,
+        # explicitly codes the path for java and the jar files.
+        scripts = ['snpEff', 'SnpSift']
+
+        for script in scripts:
+            script_sh = join_path(os.path.dirname(__file__), script + ".sh")
+            script_path = join_path(prefix.bin, script)
+            install(script_sh, script_path)
+            set_executable(script_path)
+
+            # 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_path, **kwargs)
+            filter_file(script + '.jar',
+                        join_path(prefix.bin, script + '.jar'),
+                        script_path, **kwargs)