I qouted this error message from galaxy, part of it:

Could not find the main class: ConvertSegemehlIraExtended_awk.  Program will 
Unable to access jarfile vispaAssemb.jar
Unable to access jarfile vispaEM.jar

From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Toqa Manasrah [tmanasr...@student.gsu.edu]
Sent: Friday, December 02, 2011 3:19 PM
To: galaxy-...@bx.psu.edu
Cc: galaxy-u...@lists.bx.psu.edu
Subject: [galaxy-dev] Define a path for the command files

Hi everybody,

I am integrating a new tool which depends on several other libraries (part of 
the tool). when galaxy run my tool, it can find main command but not the 
deepest. where should I define the path of the libraries and command folders I 
need. by teh way, all these commands and libraries are copied inside the tool 

Thank you,
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