Hi,
I am new to Galaxy and have not found a solution on dev-list to this 8-bit bytestrings error. That occurs on my local installation but not on Galaxy main server.
Cheers
Dataset generation errors
*Dataset 22: Neighbor Joining Tree on data 20*
The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File "/data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 123, in run_job job_wrapper.finish( stdout, stderr ) File "/data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/__init__.py", line 573, in finish self.sa_session.flush() File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1434, in _flush flush_context.execute() File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute UOWExecutor().execute(self, tasks) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute self.execute_save_steps(trans, task) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 773, in execute_save_steps self.execute_cyclical_dependencies(trans, task, False) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 789, in execute_cyclical_dependencies self.execute(trans, [t], isdelete) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute self.execute_save_steps(trans, task) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps self.save_objects(trans, task) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE history_dataset_association SET update_time=?, info=?, blurb=?, peek=? WHERE history_dataset_association.id = ?' ['2012-09-04 06:23:08.928377', 'Single Alignment Analyses\nsh: /data/APPLIS/GALAXY/galaxy-dist/tool-data/HYPHY/HYPHY: Aucun fichier ou r\xc3\xa9pertoire de ce type\n', 'error', 'no peek', 55]