Hello Michael,

Environment variables properly defined in a tool's associated 
tool_dependencies.xml file contained in an installed Tool Shed repository 
should be available to the tool's environment at runtime.  Do you have an 
example where you are not seeing this?

Greg Von Kuster

On Mar 21, 2014, at 1:22 PM, Michael E. Cotterell <mepcotter...@gmail.com> 
wrote:

> Is the expected behavior that environmental variables setup in a tool’s 
> tool_dependencies.xml file are not available in the tool’s python virtualenv 
> during runtime? It’s seems odd that we can specify modules (installable from 
> pip) that are available during runtime, but that the environmental variables 
> are not available during runtime.  
> 
> Thanks!  
> 
> Sincerely,
> Michael E. Cotterell
> 
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> Department Liaison, CS Graduate Student Association, University of Georgia
> mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
> mepc...@uga.edu (mailto:mepc...@uga.edu)
> m...@cs.uga.edu (mailto:m...@cs.uga.edu)
> http://michaelcotterell.com/
> 
> 
> 
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