Hi Tomas,

I am going to move your question over to the galaxy-...@bx.psu.edu mailing list, which give it better exposure to the development community. This is where you will also want to post questions about local installs going forward. Someone here may have advice about this tool - but really your best bet is with the tool/wrapper author.


I checked the Galaxy Main Tool Shed, and the repository there for this tool shows it is inactive/never downloaded in the current tool shed version. So, this was not your source or you obtained it some time ago (~ 2 yrs). Still, if this was your source/version, log into the Tool Shed, click on "Repository Actions", and contact the repo owner:
http://toolshed.g2.bx.psu.edu/view/petr-novak/repeatrxplorer
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contacting_the_owner_of_a_repository

This is another link to the tool author for the Main Tool Shed wrapper and the primary tool itself, and perhaps for the wrapper version you are working with as well (from some other source, but you will have to check):
http://repeatexplorer.umbr.cas.cz/static/html/help/manual.html

Good luck!

Jen
Galaxy team

On 2/28/13 12:34 AM, Thomas Muench wrote:
Hi,

i have installed RepeatExplorer on our local galaxy instance, but with every 
try, i see only this error message and i don't know why? All installation steps 
of RepeatExplorer was correctly.

Thank you for your help

Thomas M√ľnch
leibniz-institute for plant genetics and crop plant research
Gatersleben, Germany


Traceback (most recent call last):
   File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 56, in run_job
     job_wrapper.prepare()
   File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 368, in prepare
     self.command_line = self.tool.build_command_line( param_dict )
   File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1524, in 
build_command_line
     command_line = fill_template( self.command, context=param_dict )
   File "/opt/galaxy/lib/galaxy/util/template.py", line 9, in fill_template
     return str( Template( source=template_text, searchList=[context] ) )
   File 
"/opt/galaxy/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
 line 1004, in __str__
     return getattr(self, mainMethName)()
   File "cheetah_DynamicallyCompiledCheetahTemplate_1362033265_04_79640.py", 
line 92, in respond
NotFound: cannot find '__root_dir__'


failure preparing job

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