Hi Dan,<div><br></div><div>Thanks for the help. The Galaxy missing tools are now loaded and working as expected.</div><div><br></div><div>Best regards,</div><div><br></div><div>Marco<br><br><div class="gmail_quote">On Thu, Jun 20, 2013 at 3:36 PM, Daniel Blankenberg <span dir="ltr">&lt;<a href="mailto:dan@bx.psu.edu" target="_blank">dan@bx.psu.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Marco,<div><br></div><div>You&#39;ll need to enable some missing tool data tables in tool_data_table_conf.xml. i.e. adding:</div>
<div><br></div><div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">    &lt;!-- Location of <span style="text-decoration:underline">Picard</span> <span style="text-decoration:underline">dict</span> files valid for GATK --&gt;</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">    &lt;table name=&quot;gatk_picard_indexes&quot; comment_char=&quot;#&quot;&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">
        &lt;columns&gt;value, <span style="text-decoration:underline">dbkey</span>, name, path&lt;/columns&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">
        &lt;file path=&quot;tool-data/gatk_sorted_picard_index.loc&quot; /&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">    &lt;/table&gt;</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">    &lt;!-- Available of GATK references --&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">
    &lt;table name=&quot;gatk_annotations&quot; comment_char=&quot;#&quot;&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">        &lt;columns&gt;value, name, gatk_value, tools_valid_for&lt;/columns&gt;</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">        &lt;file path=&quot;tool-data/gatk_annotations.txt&quot; /&gt;</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 11px/normal Monaco">
    &lt;/table&gt;</div></div><div><br></div><div>Also make sure the files exist at the listed &lt;file path&gt;, they probably do, but if not, there are *.sample files in the tool-data you can copy over.</div><div><br></div>
<div><br></div><div>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).</div>
<div><br></div><div><br></div><div><br></div><div>Thanks for using Galaxy,</div><div><br></div><div>Dan</div><div><br></div><div><br><div><div><div class="h5"><div>On Jun 20, 2013, at 2:19 PM, Marco Ocana wrote:</div><br>
</div></div><blockquote type="cite"><div><div class="h5">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>
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