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 ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/