Hi Peter, Yes, this is a known recent issue that I'm actually at work fixing right now. -Dannon On Tue Feb 24 2015 at 9:53:24 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:

Hi all,

I'm trying the (BETA 2) GitHub repository with a view to switching from hg for my Galaxy development. There are a couple of big scary tracebacks in the stdout which look like SQLalchemy incompatibilities - are these a recent issue?

$ git clone $ cd galaxy $ cp config/galaxy.ini.sample config/galaxy.ini $ emacs config/galaxy.ini (set port and a few misc settings like admin users) $ ./run.sh ... galaxy.jobs.handler DEBUG 2015-02-24 14:49:20,223 Loaded job runners plugins: lwr:local galaxy.jobs.handler INFO 2015-02-24 14:49:20,224 job handler stop queue started galaxy.jobs.handler INFO 2015-02-24 14:49:20,238 job handler queue started galaxy.sample_tracking.external_service_types ERROR 2015-02-24 14:49:20,240 error reading external_service_type from path: simple_unknown_sequencer.xml Traceback (most recent call last): File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 32, in load_all external_service_type = self.load_external_service_type( os.path.join( self.root_dir, file_path ), visible ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 43, in load_external_service_type return ExternalServiceType( config_file, root, visible ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 60, in __init__ self.parse( root ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 78, in parse self.form_definition = form_factory.from_elem( root.find( 'form' ) ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", line 59, in from_elem return self.new( form_type, name, description=description, fields=fields, layout=layout, form_definition_current=form_definition_current ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", line 32, in new rval = FormDefinition( name=name, desc=description, form_type=self.form_types[form_type], form_definition_current=form_definition_current, layout=layout, fields=fields ) File "<string>", line 4, in __init__ File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py", line 260, in _initialize_instance return manager.original_init(*mixed[1:], **kwargs) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/__init__.py", line 3417, in __init__ self.fields = fields File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 226, in __set__ instance_dict(instance), value, None) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 693, in set value, old, initiator) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 712, in fire_replace_event state, value, previous, initiator or self._replace_token) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", line 445, in set value = cls.coerce(key, value) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/custom_types.py", line 48, in coerce return Mutable.coerce(key, value) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", line 403, in coerce raise ValueError(msg % (key, type(value))) ValueError: Attribute 'fields' does not accept objects of type <type 'list'> galaxy.sample_tracking.external_service_types ERROR 2015-02-24 14:49:20,244 error reading external_service_type from path: applied_biosystems_solid.xml Traceback (most recent call last): File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 32, in load_all external_service_type = self.load_external_service_type( os.path.join( self.root_dir, file_path ), visible ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 43, in load_external_service_type return ExternalServiceType( config_file, root, visible ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 60, in __init__ self.parse( root ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ tracking/external_service_types.py", line 78, in parse self.form_definition = form_factory.from_elem( root.find( 'form' ) ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", line 59, in from_elem return self.new( form_type, name, description=description, fields=fields, layout=layout, form_definition_current=form_definition_current ) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", line 32, in new rval = FormDefinition( name=name, desc=description, form_type=self.form_types[form_type], form_definition_current=form_definition_current, layout=layout, fields=fields ) File "<string>", line 4, in __init__ File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py", line 260, in _initialize_instance return manager.original_init(*mixed[1:], **kwargs) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/__init__.py", line 3417, in __init__ self.fields = fields File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 226, in __set__ instance_dict(instance), value, None) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 693, in set value, old, initiator) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 712, in fire_replace_event state, value, previous, initiator or self._replace_token) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", line 445, in set value = cls.coerce(key, value) File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/custom_types.py", line 48, in coerce return Mutable.coerce(key, value) File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", line 403, in coerce raise ValueError(msg % (key, type(value))) ValueError: Attribute 'fields' does not accept objects of type <type 'list'> galaxy.workflow.scheduling_manager DEBUG 2015-02-24 14:49:20,247 Starting workflow schedulers ... Starting server in PID 360. serving on http://127.0.0.1:8081

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