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'
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