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'
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