Michael,

I've tested your tool_dependencies.xml definition locally, and verified that the JAVA_HOME variable is available within the virtualenv it sets up. In order to help narrow down the source of this issue, could you provide 5 lines before and after the following line in your paster log, when attempting to run a tool that uses this tool dependency?

galaxy.tools.deps DEBUG 2014-03-25 08:52:54,953 Building dependency shell command for dependency 'wsextensions_deps'


   --Dave B.

On 03/21/2014 01:22 PM, Michael E. Cotterell 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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