From 4ba3c81bc84a7cacbd3a8d159b22eacc031baca9 Mon Sep 17 00:00:00 2001
From: Levi Baber <baberlevi@gmail.com>
Date: Tue, 6 Nov 2018 08:36:47 -0600
Subject: snpeff: add wrapper for SnpSift.jar (#9674)

---
 var/spack/repos/builtin/packages/snpeff/SnpSift.sh |  3 ++
 var/spack/repos/builtin/packages/snpeff/package.py | 32 ++++++++++++----------
 2 files changed, 21 insertions(+), 14 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/snpeff/SnpSift.sh

diff --git a/var/spack/repos/builtin/packages/snpeff/SnpSift.sh b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh
new file mode 100644
index 0000000000..3422a77914
--- /dev/null
+++ b/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 "$@"
diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py
index 046ad49e52..81e7147d20 100644
--- a/var/spack/repos/builtin/packages/snpeff/package.py
+++ b/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)
-
-        # 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)
+        # 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)
-- 
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