Importing workflow from file fails in Galaxy instance on Amazon Cloud
Hi, I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this? Thanks, Sébastien Internal Server Error
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 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:190 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
Galaxy was unable to sucessfully complete your request URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow Module galaxy.web.framework.middleware.error:149 in __call__ source=src,add_to_menu=add_to_menu ) Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict
module = module_factory.from_dict( trans, step_dict, secure=False ) Module galaxy.workflow.modules:428 in from_dict return self.module_types[type].from_dict( trans, d, **kwargs ) Module galaxy.workflow.modules:222 in from_dict module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) Module galaxy.tools:849 in decode self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) Module galaxy.tools.parameters:92 in params_from_strings value = json_fix( from_json_string( value ) ) Module simplejson:384 in loads Module simplejson.decoder:402 in decode TypeError: expected string or buffer
Sébastien, This seems to be a galaxy bug from a little while back. To fix your cloud instance, go to the cloud admin console and click "Update Galaxy", and the problem should be resolved once galaxy updates and restarts. -Dannon On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau < sebastien.vigneau@gmail.com> wrote:
Hi,
I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this?
Thanks,
Sébastien
Internal Server Error
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 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:190 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
Galaxy was unable to sucessfully complete your request URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow Module galaxy.web.framework.middleware.error:149 in __call__ source=src,add_to_menu=add_to_menu ) Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict
module = module_factory.from_dict( trans, step_dict, secure=False ) Module galaxy.workflow.modules:428 in from_dict return self.module_types[type].from_dict( trans, d, **kwargs ) Module galaxy.workflow.modules:222 in from_dict module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) Module galaxy.tools:849 in decode self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) Module galaxy.tools.parameters:92 in params_from_strings value = json_fix( from_json_string( value ) ) Module simplejson:384 in loads Module simplejson.decoder:402 in decode TypeError: expected string or buffer
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
participants (2)
-
Dannon Baker -
Sébastien Vigneau