Hi Alex, Thanks for reporting this error. This is likely caused by the change in type for one of the parameters used in the tool between when the original job was run and when the workflow extraction was attempted. I've committed a fix in changeset 8169:6ff28399645a and also added a warning message when extracting workflows that have differences in tool versions in changeset 8170:4ce18911037c.
If this isn't the likely cause (the original tool run was recent and the extraction was performed with the same tool version) or if you still have the issue after apply the fix, please let us know. Thanks for using Galaxy, Dan On Nov 6, 2012, at 5:51 PM, Oleksandr Moskalenko wrote: > Hi, > > I wonder if it's a known problem. I had a quick look through the mailing > list, but didn't see any relevant messages: > > > An extraction of a workflow from a history breaks on the bwa step: > > Error - <type 'exceptions.ValueError'>: invalid literal for int() with base > 10: 'False' > URL: http://galaxy.hpc.ufl.edu/workflow/build_from_current_history > File > '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 > in __call__ > return self.application(environ, start_response) > File '/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', > line 91 in __call__ > return self.app( environ, start_response ) > File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ > body = method( trans, **kwargs ) > File '/galaxy/run/prod/lib/galaxy/web/controllers/workflow.py', line 1253 in > build_from_current_history > param_values = job.get_param_values( trans.app ) > File '/galaxy/run/prod/lib/galaxy/model/__init__.py', line 263 in > get_param_values > param_dict = tool.params_from_strings( param_dict, app, > ignore_errors=ignore_errors ) > File '/galaxy/run/prod/lib/galaxy/tools/__init__.py', line 2041 in > params_from_strings > return params_from_strings( self.inputs, params, app, ignore_errors ) > File '/galaxy/run/prod/lib/galaxy/tools/parameters/__init__.py', line 94 in > params_from_strings > value = params[key].value_from_basic( value, app, ignore_errors ) > File '/galaxy/run/prod/lib/galaxy/tools/parameters/grouping.py', line 462 in > value_from_basic > rval[ input.name ] = input.value_from_basic( value[ input.name ], app, > ignore_errors ) > File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 136 in > value_from_basic > return self.to_python( value, app ) > File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 267 in > to_python > raise err > ValueError: invalid literal for int() with base 10: 'False' > > > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/
