Just an update on that. I found out that if I put back the migrated_tool_conf.xml and shed_tool_conf.xml back in the galaxy_dist root, I can now reset metadata on most of the repositories (but not all) Same error as before pops up in paster.log for those not working. Cheers! Yves Gagnon From: Yves Gagnon <yves.gagnon@dnalandmarks.ca> To: <galaxy-dev@lists.galaxyproject.org> Date: 20/01/2015 03:26 PM Subject: [galaxy-dev] Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories Sent by: galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.org> 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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/