Hi Marine
Could you please provide the tool definition xml file. Otherwise it is going to be difficult to guess, what is going wrong
Regards, Hans
On 05/30/2012 11:10 AM, Marine Rohmer wrote:
Hi everyone,
I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the <command>, <param> etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface.
However, when I execute my tool, Galaxy says to me :
Error executing tool: cannot find 'database'
And in my shell, I can see :
127.0.0.1 - - [30/May/2012:10:47:01 +0200] "GET /tool_runner?tool_id=myTool HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 333, in execute data.name = fill_template( output.label, context=params ) File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=myTool" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0"
I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04)
All help will be very very appreciated !
Thank you,
Marine
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