Hello Mike,
I am going to move your question over to the galaxy-...@bx.psu.edu
mailing list, which is for the discussion of local instance questions.
Some things to double check:
SAMTools is already set up correctly, with indexes?
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
-> see "SAM Tools installation"
If you are still running pile-up, note that two versions of SAMTools are
required:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
Including some reorganization to accommodate both versions, as explained
in this wiki:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Hopefully this helps,
Best,
Jen
Galaxy team
On 3/1/12 5:49 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?
Thanks,
Mike Waldron
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