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 <d...@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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