Hello fellow galaxy users : I noticed that trying to install some tools from the main toolshed, sometimes it works, others it does not. In a specific case, trying to install clustalw and its dependency, I get this error message : URL: (redactedURL)/admin_toolshed/prepare_for_install File '(redacted path)/galaxy_dist_dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File '(redacted path)/galaxy_dist_dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1095 in prepare_for_install install_repository_manager.handle_tool_shed_repositories( installation_dict, using_api=False ) File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/install_manager.py', line 636 in handle_tool_shed_repositories new_tool_panel_section_label=new_tool_panel_section_label ) File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py', line 200 in create_repository_dependency_objects self.app.installed_repository_manager.activate_repository( repository_db_record ) File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/installed_repository_manager.py', line 90 in activate_repository repository_tools_tups = irmm.get_repository_tools_tups() File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 69 in get_repository_tools_tups index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) TypeError: 'NoneType' object is not iterable Same goes for resetting all metadata on installed repositories after update, 23 out of ~200 tools work, for the rest I get this error in paster.log : tool_shed.galaxy_install.metadata.installed_repository_metadata_manager ERROR 2015-01-20 15:18:35,357 Error attempting to reset metadata on repository tabular_to_fasta Traceback (most recent call last): File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 114, in reset_metadata_on_selected_repositories self.set_repository( repository ) File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 142, in set_repository super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) File "(redacted path)/galaxy_dist_dev/lib/tool_shed/metadata/metadata_generator.py", line 1066, in set_repository self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } AttributeError: 'NoneType' object has no attribute 'get' My galaxy contains this line for tool_conf files, and I moved all config files from the distrib root to the config folder: tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml Did I do something wrong while updating to the latest releases??? Thanks for your help! Yves Gagnon