On Mon, Oct 24, 2011 at 11:17 AM, michael burrell (TOC) <michael.burrell@nbi.ac.uk> wrote:
Good Morning, I am just in the process of updating our development galaxy, the following issues are been reported and I am unable to resolved them, would anyone have any suggestions.
Just a little more background info,
galaxy@jic55666:~/software/galaxy-central$ hg tip
changeset: 6143:6c8695c2a949 tag: tip user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Oct 19 16:47:25 2011 -0400 summary: Enhanced Galaxy instance <=> Galaxy tool shed integration:
galaxy@jic55666:~/software/galaxy-central$ python --version
Python 2.6.6
the errors reported….
====
galaxy.tools DEBUG 2011-10-20 13:18:47,691 Loaded tool: hmmscan 1.0.0
docutils WARNING 2011-10-20 13:18:47,697 <string>:2: (WARNING/2) Inline strong start-string without end-string.
docutils WARNING 2011-10-20 13:18:47,700 <string>:17: (ERROR/3) Unexpected indentation.
====
galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt
Traceback (most recent call last):
File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 106, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 186, in load_tool
tree = util.parse_xml( config_file )
File "/home/galaxy/software/galaxy-central/lib/galaxy/util/__init__.py", line 105, in parse_xml
tree = ElementTree.parse(fname)
File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse
parser.feed(data)
File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed
self._parser.Parse(data, 0)
ExpatError: syntax error: line 1, column 0
That looks like a XML error from something associated with one of my wrappers on the Tool Shed (nlstradamus). Is that something you've installed locally? Was it running fine before updating Galaxy? Do you have any other tools from the Tool Shed and are they working? I haven't yet updated our local install since all the Tool Shed Integration stuff started happening. Peter