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….

 

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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

 

====

 

galaxy.tools DEBUG 2011-10-20 13:18:50,172 Loaded tool: tophat 1.5.0

docutils WARNING 2011-10-20 13:18:50,208 <string>:50: (WARNING/2) Literal block expected; none found.

 

galaxy.tools.test DEBUG 2011-10-20 13:18:50,221 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first.

galaxy.tools.test DEBUG 2011-10-20 13:18:50,222 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first.

galaxy.tools DEBUG 2011-10-20 13:18:50,222 Loaded tool: tophat_color 1.0.0

galaxy.tools DEBUG 2011-10-20 13:18:50,255 Loaded tool: cufflinks 0.0.5

galaxy.tools DEBUG 2011-10-20 13:18:50,428 Loaded tool: cuffcompare 0.0.5

galaxy.tools DEBUG 2011-10-20 13:18:50,462 Loaded tool: cuffdiff 0.0.5

 

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galaxy.tools DEBUG 2011-10-20 13:18:51,301 Loaded tool: rgManQQ1 1.0.3

galaxy.tools.test DEBUG 2011-10-20 13:18:51,323 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first.

 

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