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
___________________________________________________________
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:
http://lists.bx.psu.edu/
