diff --git a/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py b/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
index ba64a1a589a..27b4b3d4b00 100644
--- a/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
+++ b/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
@@ -3,7 +3,7 @@ import os
 import shutil
 import sys
 
-sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, 'lib' ) )
 
 from tool_shed.util.basic_util import INSTALLATION_LOG
 
diff --git a/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py b/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
index 1c4c31ff394..ff3c1114e74 100644
--- a/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
+++ b/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
@@ -2,7 +2,7 @@ import argparse
 import os
 import sys
 
-sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, 'lib' ) )
 
 import boto
 
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index 3f090f2edba..164db8f197c 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py
@@ -11,11 +11,11 @@ from datetime import datetime, timedelta
 from time import strftime
 from optparse import OptionParser
 
-sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
-
 import sqlalchemy as sa
 from sqlalchemy import and_, distinct, false, not_
 
+sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, 'lib' ) )
+
 import galaxy.webapps.tool_shed.config as tool_shed_config
 import galaxy.webapps.tool_shed.model.mapping
 from galaxy.util import send_mail as galaxy_send_mail
diff --git a/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py b/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
index bae248d5b7c..31e374e7ff1 100644
--- a/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
+++ b/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
@@ -2,7 +2,7 @@ import argparse
 import os
 import sys
 
-sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, 'lib' ) )
 
 import galaxy.config as galaxy_config
 import galaxy.model