diff --git a/config/tool_shed.ini.sample b/config/tool_shed.ini.sample
index a30c816c254..a747bd3e0b7 100644
--- a/config/tool_shed.ini.sample
+++ b/config/tool_shed.ini.sample
@@ -46,6 +46,14 @@ session_data_dir = %(here)s/database/beaker_sessions
 session_key = galaxysessions
 session_secret = changethisinproduction
 
+# -- Repository and Tool search
+# Using the script located at scripts/build_ts_whoosh_index.py
+# you can generate search index and allow full text API searching over
+# the repositories and tools within the Tool Shed given that you specify
+# the following two config options.
+toolshed_search_on = True
+whoosh_index_dir = database/toolshed_whoosh_indexes
+
 # -- Analytics
 
 # You can enter tracking code here to track visitor's behavior
diff --git a/lib/galaxy/webapps/tool_shed/config.py b/lib/galaxy/webapps/tool_shed/config.py
index 34af979b53c..da81bea7d15 100644
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -43,8 +43,8 @@ class Configuration( object ):
         self.database_engine_options = get_database_engine_options( kwargs )
         self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) )
         # Whoosh search
-        self.toolshed_search_on = string_as_bool( kwargs.get( "toolshed_search_on", False ) )
-        self.toolshed_whoosh_index_dir = kwargs.get( "toolshed_whoosh_index_dir", None )
+        self.toolshed_search_on = string_as_bool( kwargs.get( "toolshed_search_on", True ) )
+        self.whoosh_index_dir = kwargs.get( "whoosh_index_dir", 'database/toolshed_whoosh_indexes' )
         # Analytics
         self.ga_code = kwargs.get( "ga_code", None )
         self.session_duration = int(kwargs.get( 'session_duration', 0 ))
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index 40f0ced29ab..d23d175a435 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -6,7 +6,9 @@ $ python scripts/tool_shed/build_ts_whoosh_index_test.py -c config/tool_shed.ini
 
 Make sure you adjusted your config to:
  * turn on searching via toolshed_search_on
- * specify toolshed_whoosh_index_dir where the indexes will be placed
+ * specify whoosh_index_dir where the indexes will be placed
+
+Also make sure that GALAXY_EGGS_PATH variable is properly set.
 """
 import sys
 import os
@@ -53,15 +55,18 @@ tool_schema = Schema(
     repo_id=STORED )
 
 
-def build_index( sa_session, toolshed_whoosh_index_dir, path_to_repositories ):
+def build_index( sa_session, whoosh_index_dir, path_to_repositories ):
     """
     Build the search indexes. One for repositories and another for tools within.
     """
-    repo_index_storage = FileStorage( toolshed_whoosh_index_dir )
-    tool_index_dir = os.path.join( toolshed_whoosh_index_dir, 'tools' )
-    #  Rare race condition exists here
+    #  Rare race condition exists here and below
+    if not os.path.exists( whoosh_index_dir ):
+        os.makedirs( whoosh_index_dir )
+    tool_index_dir = os.path.join( whoosh_index_dir, 'tools' )
     if not os.path.exists( tool_index_dir ):
         os.makedirs( tool_index_dir )
+
+    repo_index_storage = FileStorage( whoosh_index_dir )
     tool_index_storage = FileStorage( tool_index_dir )
 
     repo_index = repo_index_storage.create_index( repo_schema )
@@ -205,5 +210,5 @@ if __name__ == "__main__":
     path_to_tool_shed_config = options.path_to_tool_shed_config
     path_to_repositories = options.path_to_repositories
     sa_session, config_settings = get_sa_session_and_needed_config_settings( path_to_tool_shed_config )
-    toolshed_whoosh_index_dir = config_settings.get( 'toolshed_whoosh_index_dir', None )
-    build_index( sa_session, toolshed_whoosh_index_dir, path_to_repositories )
+    whoosh_index_dir = config_settings.get( 'whoosh_index_dir', None )
+    build_index( sa_session, whoosh_index_dir, path_to_repositories )