diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py
index 09916169..c4e46e19 100644
--- a/repo2docker/__main__.py
+++ b/repo2docker/__main__.py
@@ -251,9 +251,10 @@ def make_r2d(argv=None):
         print(__version__)
         sys.exit(0)
 
-    args = get_argparser().parse_args(argv)
+    args, traitlet_args = get_argparser().parse_known_args(argv)
 
     r2d = Repo2Docker()
+    r2d.parse_command_line(traitlet_args)
 
     if args.debug:
         r2d.log_level = logging.DEBUG
diff --git a/repo2docker/app.py b/repo2docker/app.py
index a03fe1df..ce49fc7f 100755
--- a/repo2docker/app.py
+++ b/repo2docker/app.py
@@ -490,7 +490,7 @@ class Repo2Docker(Application):
             extra=dict(phase="failed"),
         )
 
-    def initialize(self):
+    def initialize(self, *args, **kwargs):
         """Init repo2docker configuration before start"""
         # FIXME: Remove this function, move it to setters / traitlet reactors
         if self.json_logs: