diff --git a/run.sh b/run.sh
index 7966f5a5e58..8d972294dd2 100755
--- a/run.sh
+++ b/run.sh
@@ -53,7 +53,9 @@ if [ $INITIALIZE_TOOL_DEPENDENCIES -eq 1 ]; then
 fi
 
 if [ -n "$GALAXY_UWSGI" ]; then
-    uwsgi $(python ./scripts/get_uwsgi_args.py)
+    uwsgi_args="$(python ./scripts/get_uwsgi_args.py)"
+    echo "executing: uwsgi $uwsgi_args"
+    uwsgi $uwsgi_args
 elif [ -n "$GALAXY_RUN_ALL" ]; then
     servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
     if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; then
diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index cf9bdd019f2..8a7e16b6c79 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -12,21 +12,46 @@ from galaxy.config import (
     parse_dependency_options,
 )
 from galaxy.script import main_factory
+from galaxy.util.properties import nice_config_parser
 
 
 DESCRIPTION = "Script to determine uWSGI command line arguments."
-COMMAND_TEMPLATE = '{virtualenv}--ini-paste {galaxy_ini} --paste-logger --die-on-term --enable-threads{mule}{farm}'
+COMMAND_TEMPLATE = '{virtualenv} --ini-paste {config_file}{processes}{threads}{http}{pythonpath}{master}{static-map}{paste-logger}{die-on-term}{enable-threads}{py-call-osafterfork}{mule}{farm}'
 
 
 def _get_uwsgi_args(args, kwargs):
+    config_file = args.config_file or kwargs['__file__']
     handlerct = int(kwargs.get('job_handler_count', 1))
-    pool_name = kwargs.get('job_handler_pool_name', 'job-handlers')
-    virtualenv = os.environ.get('VIRTUAL_ENV', None)
-    print(COMMAND_TEMPLATE.format(
-        virtualenv='--virtualenv %s ' % virtualenv if virtualenv else '',
-        galaxy_ini=args.config_file or kwargs['__file__'],
-        mule=' --py-call-osafterfork' + ' --mule=lib/galaxy/main.py' * handlerct if handlerct else '',
-        farm=' --farm=%s:%s' % (pool_name, ','.join([str(x) for x in range(1, handlerct + 1)]))))
+    config = nice_config_parser(config_file)
+    config_defaults = {
+        'virtualenv': ' --virtualenv {venv}'.format(venv=os.environ.get('VIRTUAL_ENV', './.venv')),
+        'processes': ' --processes 1',
+        'threads': ' --threads 4',
+        'http': ' --http localhost:8080',
+        'pythonpath': ' --pythonpath lib',
+        'master': ' --master',
+        'static-map': (' --static-map /static/style={here}/static/style/blue'
+                       ' --static-map /static={here}/static'.format(here=os.getcwd())),
+        'paste-logger': ' --paste-logger',
+        'die-on-term': ' --die-on-term',
+        'enable-threads': ' --enable-threads',
+        'py-call-osafterfork': ' --py-call-osafterfork',
+        'mule': ' --mule=lib/galaxy/main.py' * handlerct,
+        'farm': ' --farm={name}:{mules}'.format(
+            name=kwargs.get('job_handler_pool_name', 'job-handlers'),
+            mules=','.join([str(x) for x in range(1, handlerct + 1)])),
+    }
+    if not config.has_section('uwsgi'):
+        format_dict = config_defaults
+    else:
+        format_dict = {}
+        for opt in config_defaults.keys():
+            if config.has_option('uwsgi', opt):
+                format_dict[opt] = ''
+            else:
+                format_dict[opt] = config_defaults[opt]
+    format_dict['config_file'] = config_file
+    print(COMMAND_TEMPLATE.format(**format_dict))
 
 
 ACTIONS = {