diff --git a/scripts/helper.py b/scripts/helper.py
index 7c5bd9c5d93..13a66a332a9 100644
--- a/scripts/helper.py
+++ b/scripts/helper.py
@@ -26,8 +26,7 @@ except:
     sys.exit( 1 )
 
 options.config = os.path.abspath( options.config )
-os.chdir( os.path.dirname( options.config ) )
-sys.path.append( 'lib' )
+sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) )
 
 from galaxy import eggs
 import pkg_resources
@@ -35,7 +34,7 @@ import pkg_resources
 config = ConfigParser( dict( file_path = 'database/files',
                              id_secret = 'USING THE DEFAULT IS NOT SECURE!',
                              database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
-config.read( os.path.basename( options.config ) )
+config.read( options.config )
 
 from galaxy.web import security
 from galaxy.model import mapping
diff --git a/scripts/set_dataset_sizes.py b/scripts/set_dataset_sizes.py
index 19692388073..d2d8390c576 100644
--- a/scripts/set_dataset_sizes.py
+++ b/scripts/set_dataset_sizes.py
@@ -13,15 +13,14 @@ parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config
 def init():
 
     options.config = os.path.abspath( options.config )
-    os.chdir( os.path.dirname( options.config ) )
-    sys.path.append( 'lib' )
+    sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) )
 
     from galaxy import eggs
     import pkg_resources
 
     config = ConfigParser( dict( file_path = 'database/files',
                                  database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
-    config.read( os.path.basename( options.config ) )
+    config.read( options.config )
 
     from galaxy.model import mapping
 
diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py
index 441dec73503..97bd6858ac7 100755
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -21,8 +21,7 @@ def init():
     if options.email == 'all':
         options.email = None
 
-    os.chdir( os.path.dirname( options.config ) )
-    sys.path.append( 'lib' )
+    sys.path.append( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) )
 
     from galaxy import eggs
     import pkg_resources
@@ -35,7 +34,7 @@ def init():
 
     config_parser = ConfigParser( dict( here = os.getcwd(),
                                         database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
-    config_parser.read( os.path.basename( options.config ) )
+    config_parser.read( options.config )
 
     config_dict = {}
     for key, value in config_parser.items( "app:main" ):