Error when trying to display data on gene track
Hello, We are running a local instance of galaxy and we get the following error when trying to display genes from our history in the ucsc browser. I got the error as I was following the galaxy 101 video in the galaxy website (last step). Thanks, --Ricardo Perez URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797 Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file extra data
full traceback URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797 Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file
Hello, The link appears to be one that is generated from this link (link to "GeneTrack"): "view in GeneTrack" Not this link (link to "UCSC Browser", same as in tutorials, and probably the one you want to be using anyway): "display at UCSC main" GeneTrack is no longer supported, although it is still present in the current distribution. It will be removed sometime soon and for now is best ignored. The link to UCSC main should be functional by default in local installations - please give this one a try and let us know if you have problems with it. Sorry for the confusion with the GeneTrack link, Jen Galaxy team On 2/20/13 11:23 AM, Perez, Ricardo wrote:
Hello,
We are running a local instance of galaxy and we get the following error when trying to display genes from our history in the ucsc browser. I got the error as I was following the galaxy 101 video in the galaxy website (last step).
Thanks, --Ricardo Perez
URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797 Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file extra data
full traceback URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797 Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file
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Perez, Ricardo