> Hi all, > > I am upgrading to the most recent galaxy-dist > 720455407d1c<https://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c> > . > First time run.sh shows following errors as in attachment. > It seems when I use 'manage_db.sh upgrade' it doesn't create necessary > tables for these tools. > Wonder if these are known issues? > > Thanks > > >
[epigraph] galaxy.tools ERROR 2011-07-05 10:34:12,556 error reading tool from path: data_destination/epigraph.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools ERROR 2011-07-05 10:34:12,559 error reading tool from path: data_destination/epigraph_test.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get'
[manipulation] galaxy.tools WARNING 2011-07-05 10:34:16,151 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. [picard] galaxy.tools ERROR 2011-07-05 10:34:16,700 error reading tool from path: picard/picard_ReorderSam.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured [mosaik] galaxy.tools ERROR 2011-07-05 10:34:17,217 error reading tool from path: sr_mapping/mosaik.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'mosaik_indexes' is required by tool but not configured [gatk] galaxy.tools ERROR 2011-07-05 10:34:17,605 error reading tool from path: gatk/realigner_target_creator.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured galaxy.tools ERROR 2011-07-05 10:34:17,612 error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured galaxy.tools ERROR 2011-07-05 10:34:17,620 error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured galaxy.tools ERROR 2011-07-05 10:34:17,628 error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured galaxy.tools DEBUG 2011-07-05 10:34:17,641 Loaded tool: gatk_analyze_covariates 0.0.1 galaxy.tools ERROR 2011-07-05 10:34:17,648 error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in parse self.parse_inputs( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 161, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 411, in __init__ "Data table named '%s' is required by tool but not configured" % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured [data_sources] galaxy.tools ERROR 2011-07-05 10:34:17,767 error reading tool from path: data_source/access_libraries.xml Traceback (most recent call last): File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get'
___________________________________________________________ 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/