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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