Revert script changes unrelated to uWSGI mule work. Includes

galaxy.util.script so that get_uwsgi_args.py still works, but that will
be PR'd separately and merged later.

scripts/get_uwsgi_args.py

@@ -8,9 +8,9 @@ from six.moves import shlex_quote
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
-from galaxy.script import main_factory
 from galaxy.util.path import get_ext
 from galaxy.util.properties import load_app_properties, nice_config_parser
+from galaxy.util.script import main_factory
 
 
 DESCRIPTION = "Script to determine uWSGI command line arguments"

scripts/manage_tool_dependencies.py

@@ -1,3 +1,4 @@
+import argparse
 import os.path
 import sys
 
@@ -9,17 +10,44 @@ from galaxy.config import (
     find_root,
     parse_dependency_options,
 )
-from galaxy.script import main_factory
 from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
+from galaxy.util.properties import find_config_file, load_app_properties
 
 DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
 
 
-def _init_if_needed(args, kwargs):
+def main(argv=None):
+    """Entry point for conversion process."""
+    if argv is None:
+        argv = sys.argv[1:]
+    args = _arg_parser().parse_args(argv)
+    action = args.action
+    action_func = ACTIONS[action]
+    action_func(args)
+
+
+def _init_if_needed(args):
+    kwargs = _app_properties(args)
+
     # If conda_auto_init is set, simply building the Conda resolver will call handle installation.
     _build_dependency_manager_no_config(kwargs)
 
 
+def _app_properties(args):
+    config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini", args.config_file)
+    app_properties = load_app_properties(ini_file=config_file)
+    return app_properties
+
+
+def _arg_parser():
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument('action', metavar='ACTION', type=str,
+                        choices=ACTIONS.keys(),
+                        help='action to perform')
+    parser.add_argument("-c", "--config-file", default=None)
+    return parser
+
+
 def _build_dependency_manager_no_config(kwargs):
     """Simplified variant of build_dependency_manager from galaxy.tools.deps.
 
@@ -56,5 +84,4 @@ ACTIONS = {
 
 
 if __name__ == '__main__':
-    main = main_factory(description=DESCRIPTION, actions=ACTIONS)
     main()