I discovered that an entry needed to be added to tool_data_table_conf.xml to define the sam_fa_indexes table the samtools_mpileup.xml was looking for. The entry points to the sam_fa_indicies.loc file. Now the Mpileup tools is enabled.

Mike Waldron

From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Waldron, Michael H [mwaldron@email.unc.edu]
Sent: Thursday, March 01, 2012 8:56 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Error trying to enable samtools_mpileup

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?


Mike Waldron