On Mar 1, 2012, at 8:49 AM, Waldron, Michael H wrote: > I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. > > I am trying to enable use of Mpileup for SAM Tools, and have added the entry > for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup > Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the > following errors from the Galaxy startup: > > galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: > samtools/samtools_mpileup.xml > Traceback (most recent call last): > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 212, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 305, in load_tool > return ToolClass( config_file, root, self.app, guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 531, in __init__ > self.parse( root, guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 641, in parse > self.parse_inputs( root ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 723, in parse_inputs > display, inputs = self.parse_input_page( page, enctypes ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 922, in parse_input_page > inputs = self.parse_input_elem( input_elem, enctypes ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 989, in parse_input_elem > case.inputs = self.parse_input_elem( case_elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 945, in parse_input_elem > group.inputs = self.parse_input_elem( elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1015, in parse_input_elem > param = self.parse_param_elem( elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1027, in parse_param_elem > param = ToolParameter.build( self, input_elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 176, in build > return parameter_types[param_type]( tool, param ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 1330, in __init__ > ToolParameter.__init__( self, tool, elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 43, in __init__ > self.validators.append( validation.Validator.from_element( self, elem ) ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", > line 23, in from_element > return validator_types[type].from_element( param, elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", > line 279, in from_element > tool_data_table = param.tool.app.tool_data_tables[ table_name ] > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line > 21, in __getitem__ > return self.data_tables.__getitem__( key ) > KeyError: 'sam_fa_indexes' > > Can someone tell me what is wrong here? Am I missing something in the > database?
Hi Mike, I moved this over to the galaxy-dev list since it pertains to a local installation. You'll need to update your tool_data_table_conf.xml from the sample. If you haven't made any modifications, the simplest solution is to just `cp tool_data_table_conf.xml.sample tool_data_table_conf.xml`. --nate > > Thanks, > > Mike Waldron > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ 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/
