Hi,<div><br></div><div>When starting up Galaxy from Cloudman and updating the latest version from repository, most of the GATK tools do not show up in the tool bar.</div><div><br></div><div>I have attached the log file.</div>
<div><br></div><div>There are other errors in the log file, but I have pasted what I believe the relavant section of the log.</div><div><br></div><div>Any pointers on how to fix the problem would be appreciated.</div><div>
<br></div><div>Thanks</div><div><br></div><div>Marco</div><div><br></div><div><div>Traceback (most recent call last):</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 396, in load_tool_tag_set</div>
<div>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 515, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 855, in __init__</div><div>    self.parse( root, guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1028, in parse</div>
<div>    self.parse_inputs( root )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1112, in parse_inputs</div><div>    display, inputs = self.parse_input_page( page, enctypes )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1516, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1583, in parse_input_elem</div>
<div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1609, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1621, in parse_param_elem</div><div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div>
<div>    return parameter_types[param_type]( tool, param )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div><div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div>
<div>    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;gatk_picard_indexes&#39;</div>
<div>galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml</div><div>Traceback (most recent call last):</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 396, in load_tool_tag_set</div>
<div>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 515, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 855, in __init__</div><div>    self.parse( root, guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1028, in parse</div>
<div>    self.parse_inputs( root )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1112, in parse_inputs</div><div>    display, inputs = self.parse_input_page( page, enctypes )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1516, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1583, in parse_input_elem</div>
<div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1609, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1621, in parse_param_elem</div><div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div>
<div>    return parameter_types[param_type]( tool, param )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div><div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div>
<div>    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;gatk_picard_indexes&#39;</div>
<div>galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml</div><div>Traceback (most recent call last):</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 396, in load_tool_tag_set</div>
<div>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 515, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 855, in __init__</div><div>    self.parse( root, guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1028, in parse</div>
<div>    self.parse_inputs( root )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1112, in parse_inputs</div><div>    display, inputs = self.parse_input_page( page, enctypes )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1516, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1583, in parse_input_elem</div>
<div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1609, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1621, in parse_param_elem</div><div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div>
<div>    return parameter_types[param_type]( tool, param )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div><div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div>
<div>    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;gatk_picard_indexes&#39;</div>
<div>galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml</div><div>Traceback (most recent call last):</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 396, in load_tool_tag_set</div>
<div>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 515, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 855, in __init__</div><div>    self.parse( root, guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1028, in parse</div>
<div>    self.parse_inputs( root )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1112, in parse_inputs</div><div>    display, inputs = self.parse_input_page( page, enctypes )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1516, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1583, in parse_input_elem</div>
<div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1609, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1621, in parse_param_elem</div><div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div>
<div>    return parameter_types[param_type]( tool, param )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div><div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div>
<div>    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;gatk_picard_indexes&#39;</div>
<div>galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml</div><div>Traceback (most recent call last):</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 396, in load_tool_tag_set</div>
<div>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 515, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 855, in __init__</div><div>    self.parse( root, guid=guid )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1028, in parse</div>
<div>    self.parse_inputs( root )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1112, in parse_inputs</div><div>    display, inputs = self.parse_input_page( page, enctypes )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1516, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1583, in parse_input_elem</div>
<div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1539, in parse_input_elem</div><div>    group.inputs = self.parse_input_elem( elem, enctypes, context )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1609, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py&quot;, line 1621, in parse_param_elem</div>
<div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div><div>    return parameter_types[param_type]( tool, param )</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div>
<div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div><div>
    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>
<div>  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;gatk_picard_indexes&#39;</div>
</div><div><br></div>