diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index e889075c615..aa9d0376bea 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -124,6 +124,9 @@ CreatedWorkflow = namedtuple("CreatedWorkflow", ["stored_workflow", "missing_too
 
 class WorkflowContentsManager(UsesAnnotations):
 
+    def __init__(self, app):
+        self.app = app
+
     def build_workflow_from_dict(
         self,
         trans,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6a9467f2a6b..d9b6db562ed 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -613,10 +613,6 @@ class Tool( object, Dictifiable ):
         """
         Read tool configuration from the element `root` and fill in `self`.
         """
-        # Get the (user visible) name of the tool
-        self.name = tool_source.parse_name()
-        if not self.name:
-            raise Exception( "Missing tool 'name'" )
         # Get the UNIQUE id for the tool
         self.old_id = tool_source.parse_id()
         if guid is None:
@@ -625,6 +621,12 @@ class Tool( object, Dictifiable ):
             self.id = guid
         if not self.id:
             raise Exception( "Missing tool 'id'" )
+
+        # Get the (user visible) name of the tool
+        self.name = tool_source.parse_name()
+        if not self.name:
+            raise Exception( "Missing tool 'name'" )
+
         self.version = tool_source.parse_version()
         if not self.version:
             # For backward compatibility, some tools may not have versions yet.
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index f9be1af8978..1aa94f23fd8 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1099,7 +1099,7 @@ class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
         Creates a workflow from a dict. Created workflow is stored in the database and returned.
         """
         # TODO: replace this method with direct access to manager.
-        workflow_contents_manager = workflows.WorkflowContentsManager()
+        workflow_contents_manager = workflows.WorkflowContentsManager( self.app )
         created_workflow = workflow_contents_manager.build_workflow_from_dict(
             trans,
             data,
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index e83528bfbc2..4e7107d44c3 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -30,7 +30,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         super( WorkflowsAPIController, self ).__init__( app )
         self.history_manager = histories.HistoryManager( app )
         self.workflow_manager = workflows.WorkflowsManager( app )
-        self.workflow_contents_manager = workflows.WorkflowContentsManager()
+        self.workflow_contents_manager = workflows.WorkflowContentsManager( app )
 
     @expose_api
     def index(self, trans, **kwd):
@@ -300,8 +300,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         """
         stored_workflow = self.__get_stored_workflow( trans, id )
         if 'workflow' in payload:
-            workflow_contents_manager = workflows.WorkflowContentsManager()
-            workflow, errors = workflow_contents_manager.update_workflow_from_dict(
+            workflow, errors = self.workflow_contents_manager.update_workflow_from_dict(
                 trans,
                 stored_workflow,
                 payload['workflow'],
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 39c2e57fc2e..d2ff8f163fe 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -106,6 +106,7 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_
         step = model.WorkflowStep()
         step.type = 'tool'
         step.tool_id = job.tool_id
+        step.tool_version = job.tool_version
         step.tool_inputs = tool_inputs
         # NOTE: We shouldn't need to do two passes here since only
         #       an earlier job can be used as an input to a later
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index c22b9ee10bd..5670084cb19 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -222,6 +222,7 @@ class SimpleWorkflowModule( WorkflowModule ):
     def save_to_step( self, step ):
         step.type = self.type
         step.tool_id = None
+        step.tool_version = None
         step.tool_inputs = self.state
 
     def get_state( self, secure=True ):