I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot. This tool creates a set of three pdf files. In older versions of Galaxy, the tool ran correctly with no problems. A recent update broke the tool. The job runs but is unable to finish. Here is the error reported:
Traceback (most recent call last): File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1015, in finish self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 158, in execute query = query % db.literal(args) File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 265, in literal return self.escape(o, self.encoders) File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 203, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position 11: ordinal not in range(256)
There is a set of files created in the job_working_directory that start with 'metadata_', some of which contain the unicode.
Is there anything I can do to fix this?
David Hoover Helix Systems Staff