Fix for tool shed handling new GenomeBuilds manager.

lib/galaxy/webapps/tool_shed/app.py

@@ -6,6 +6,7 @@ import galaxy.quota
 import galaxy.datatypes.registry
 import galaxy.webapps.tool_shed.model
 from galaxy.openid.providers import OpenIDProviders
+from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web import security
 from galaxy.tags.tag_handler import CommunityTagHandler
 from tool_shed.grids.util import RepositoryGridFilterManager
@@ -49,6 +50,7 @@ class UniverseApplication( object ):
         # Initialize the Tool Shed tool data tables.  Never pass a configuration file here
         # because the Tool Shed should always have an empty dictionary!
         self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path )
+        self.genome_builds = GenomeBuilds( self )
         # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
         self.toolbox = tools.ToolBox( [], self.config.tool_path, self )
         # Initialize the Tool Shed security agent.

lib/galaxy/webapps/tool_shed/config.py

@@ -53,6 +53,7 @@ class Configuration( object ):
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() )
         self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
         self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
+        self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root )
         self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
         # Install and test framework for testing tools contained in repositories.
         self.num_tool_test_results_saved = kwargs.get( 'num_tool_test_results_saved', 5 )