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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