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

====

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

====

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.

=========
-----------------------------------------------------------------------------------------------------
Please note, that my email address is no longer givenname.surn...@bbsrc.ac.uk.  
Please update your records to reflect my new email address of 
givenname.surn...@nbi.ac.uk as shown on this email.
___________________________________________________________
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/

Reply via email to