1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9b33b543fb14/ Changeset: 9b33b543fb14 User: dan Date: 2014-05-19 21:35:58 Summary: Fix for tool shed handling new GenomeBuilds manager. Affected #: 2 files
diff -r 3faf01e5111ecf454f06b22546b530131b0550be -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -6,6 +6,7 @@ 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 @@ # 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.
diff -r 3faf01e5111ecf454f06b22546b530131b0550be -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -53,6 +53,7 @@ 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 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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