GATK tools not showing up in cloudman Galaxy installation
Hi, 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. I have attached the log file. There are other errors in the log file, but I have pasted what I believe the relavant section of the log. Any pointers on how to fix the problem would be appreciated. Thanks Marco Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1539, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'
Hi Marco, You'll need to enable some missing tool data tables in tool_data_table_conf.xml. i.e. adding: <!-- Location of Picard dict files valid for GATK --> <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/gatk_sorted_picard_index.loc" /> </table> <!-- Available of GATK references --> <table name="gatk_annotations" comment_char="#"> <columns>value, name, gatk_value, tools_valid_for</columns> <file path="tool-data/gatk_annotations.txt" /> </table> Also make sure the files exist at the listed <file path>, they probably do, but if not, there are *.sample files in the tool-data you can copy over. From the Galaxy root, doing a diff tool_data_table_conf.xml tool_data_table_conf.xml.sample should show any other missing data table entries (along with the differences in custom paths to certain data). Thanks for using Galaxy, Dan On Jun 20, 2013, at 2:19 PM, Marco Ocana wrote:
Hi,
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.
I have attached the log file.
There are other errors in the log file, but I have pasted what I believe the relavant section of the log.
Any pointers on how to fix the problem would be appreciated.
Thanks
Marco
Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1539, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'
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Hi Dan, Thanks for the help. The Galaxy missing tools are now loaded and working as expected. Best regards, Marco On Thu, Jun 20, 2013 at 3:36 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Marco,
You'll need to enable some missing tool data tables in tool_data_table_conf.xml. i.e. adding:
<!-- Location of Picard dict files valid for GATK --> <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/gatk_sorted_picard_index.loc" /> </table> <!-- Available of GATK references --> <table name="gatk_annotations" comment_char="#"> <columns>value, name, gatk_value, tools_valid_for</columns> <file path="tool-data/gatk_annotations.txt" /> </table>
Also make sure the files exist at the listed <file path>, they probably do, but if not, there are *.sample files in the tool-data you can copy over.
From the Galaxy root, doing a diff tool_data_table_conf.xml tool_data_table_conf.xml.sample should show any other missing data table entries (along with the differences in custom paths to certain data).
Thanks for using Galaxy,
Dan
On Jun 20, 2013, at 2:19 PM, Marco Ocana wrote:
Hi,
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.
I have attached the log file.
There are other errors in the log file, but I have pasted what I believe the relavant section of the log.
Any pointers on how to fix the problem would be appreciated.
Thanks
Marco
Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1539, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'
<galaxy.log>___________________________________________________________ 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/
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participants (2)
-
Daniel Blankenberg -
Marco Ocana