snpeff: add wrapper for SnpSift.jar (#9674)

var/spack/repos/builtin/packages/snpeff/SnpSift.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the SnpSift jar file
+java -jar SnpSift.jar "$@"

var/spack/repos/builtin/packages/snpeff/package.py

@@ -22,17 +22,21 @@ class Snpeff(Package):
     def install(self, spec, prefix):
         install_tree('snpEff', 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__), "snpEff.sh")
-        script = prefix.bin.snpEff
-        install(script_sh, script)
-        set_executable(script)
+        # 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']
 
-        # 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, **kwargs)
-        filter_file('snpEff.jar', join_path(prefix.bin, 'snpEff.jar'),
-                    script, **kwargs)
+        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)