Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories

20 Jan 2015

      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

Yves Gagnon

Yves Gagnon

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