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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___________________________________________________________
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

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please use the interface at:

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