On Mon, Oct 24, 2011 at 11:17 AM, michael burrell (TOC)
<michael.burr...@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 <g...@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

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