On Jun 4, 2012, at 11:34 AM, Shantanu Pavgi wrote:

> 
> I am getting following errors in the galaxy log:
> 
> {{{
> Error reading tool from path: human_genome_variation/sift.xml
> Traceback (most recent call last):
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py", line 
> 315, in load_tool_tag_set
>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py", line 
> 420, in load_tool
>    tree = util.parse_xml( config_file )
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/util/__init__.py", line 
> 105, in parse_xml
>    tree = ElementTree.parse(fname)
>  File 
> "/home/shantanu/galaxy/galaxy-uab/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 859, in parse
>    tree.parse(source, parser)
>  File 
> "/home/shantanu/galaxy/galaxy-uab/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 576, in parse
>    source = open(source, "rb")
> IOError: [Errno 2] No such file or directory: 
> './tools/human_genome_variation/sift.xml'
> galaxy.tools ERROR 2012-06-04 09:57:18,028 Error reading tool from path: 
> human_genome_variation/linkToGProfile.xml
> Traceback (most recent call last):
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py", line 
> 315, in load_tool_tag_set
>    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py", line 
> 420, in load_tool
>    tree = util.parse_xml( config_file )
>  File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/util/__init__.py", line 
> 105, in parse_xml
>    tree = ElementTree.parse(fname)
>  File 
> "/home/shantanu/galaxy/galaxy-uab/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 859, in parse
>    tree.parse(source, parser)
>  File 
> "/home/shantanu/galaxy/galaxy-uab/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 576, in parse
>    source = open(source, "rb")
> 
> }}}
> 
> This tool was renamed or moved in the latest galaxy-dist update. So I think 
> the error should get resolved after removing corresponding 'hgv' entry from 
> tool_conf.xml file. Is that correct way to resolve it or do I need to perform 
> any other/additional steps?

That's correct.  These tools are now available through the Tool Shed.

--nate

> 
> 
> --
> Thanks,
> Shantanu
> 
> 
> 
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