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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