diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 607118a83bc..60e515ea221 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -31,6 +31,11 @@ app = None
 class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
     """Encapsulates the state of a Universe application"""
     def __init__( self, **kwargs ):
+        if not log.handlers:
+            # Paste didn't handle it, so we need a temporary basic log
+            # configured.  The handler added here gets dumped and replaced with
+            # an appropriately configured logger in configure_logging below.
+            logging.basicConfig(level=logging.DEBUG)
         log.debug( "python path is: %s", ", ".join( sys.path ) )
         self.name = 'galaxy'
         self.new_installation = False
@@ -39,7 +44,7 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
         self.config.check()
         config.configure_logging( self.config )
         self.configure_fluent_log()
-
+        self.config.reload_sanitize_whitelist(explicit='sanitize_whitelist_file' in kwargs)
         self.amqp_internal_connection_obj = galaxy.queues.connection_from_config(self.config)
         # control_worker *can* be initialized with a queue, but here we don't
         # want to and we'll allow postfork to bind and start it.
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index f7627d5580a..264a22e216b 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -259,7 +259,6 @@ class Configuration( object ):
         self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root )
-        self.reload_sanitize_whitelist()
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
@@ -473,7 +472,7 @@ class Configuration( object ):
         else:
             return None
 
-    def reload_sanitize_whitelist( self ):
+    def reload_sanitize_whitelist( self, explicit=True ):
         self.sanitize_whitelist = []
         try:
             with open(self.sanitize_whitelist_file, 'rt') as f:
@@ -481,7 +480,8 @@ class Configuration( object ):
                     if not line.startswith("#"):
                         self.sanitize_whitelist.append(line.strip())
         except IOError:
-            log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
+            if explicit:
+                log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
 
     def __parse_config_file_options( self, kwargs ):
         """