diff --git a/lib/galaxy/jobs/runners/lwr.py b/lib/galaxy/jobs/runners/lwr.py
index 60c29cd5e46..ac9d7ca40ab 100644
--- a/lib/galaxy/jobs/runners/lwr.py
+++ b/lib/galaxy/jobs/runners/lwr.py
@@ -69,7 +69,8 @@ class LwrJobRunner( AsynchronousJobRunner ):
             output_files = self.get_output_files(job_wrapper)
             input_files = job_wrapper.get_input_fnames()
             working_directory = job_wrapper.working_directory
-            file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory)
+            tool = job_wrapper.tool
+            file_stager = FileStager(client, tool, command_line, job_wrapper.extra_filenames, input_files, output_files, working_directory)
             rebuilt_command_line = file_stager.get_rewritten_command_line()
             job_id = file_stager.job_id
             client.launch( rebuilt_command_line )
@@ -228,4 +229,4 @@ class LwrJobRunner( AsynchronousJobRunner ):
         elif job.get_state() == model.Job.states.QUEUED:
             # LWR doesn't queue currently, so this indicates galaxy was shutoff while 
             # job was being staged. Not sure how to recover from that. 
-            job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted.  Please retry the job." )
\ No newline at end of file
+            job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted.  Please retry the job." )
diff --git a/lib/galaxy/jobs/runners/lwr_client/__init__.py b/lib/galaxy/jobs/runners/lwr_client/__init__.py
index b2d74255b81..847bfc9d823 100644
--- a/lib/galaxy/jobs/runners/lwr_client/__init__.py
+++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py
@@ -132,7 +132,7 @@ class FileStager(object):
 
     """
 
-    def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory):
+    def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory):
         """
         """
         self.client = client
@@ -140,7 +140,9 @@ class FileStager(object):
         self.config_files = config_files
         self.input_files = input_files
         self.output_files = output_files
-        self.tool_dir = os.path.abspath(tool_dir)
+        self.tool_id = tool.id
+        self.tool_version = tool.version
+        self.tool_dir = os.path.abspath(tool.tool_dir)
         self.working_directory = working_directory
 
         # Setup job inputs, these will need to be rewritten before
@@ -161,7 +163,7 @@ class FileStager(object):
         self.__upload_rewritten_config_files()
 
     def __handle_setup(self):
-        job_config = self.client.setup()
+        job_config = self.client.setup(self.tool_id, self.tool_version)
 
         self.new_working_directory = job_config['working_directory']
         self.new_outputs_directory = job_config['outputs_directory']
@@ -480,11 +482,16 @@ class Client(object):
         self.__raw_execute("clean", {"job_id": self.job_id})
 
     @parseJson()
-    def setup(self):
+    def setup(self, tool_id=None, tool_version=None):
         """
         Setup remote LWR server to run this job.
         """
-        return self.__raw_execute("setup", {"job_id": self.job_id})
+        setup_args = {"job_id": self.job_id}
+        if tool_id:
+            setup_args["tool_id"] = tool_id
+        if tool_version:
+            setup_args["tool_version"] = tool_version
+        return self.__raw_execute("setup", setup_args)
 
 
 def _read(path):