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? -- Thanks, Shantanu
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Nate Coraor -
Shantanu Pavgi