[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'