Re: [galaxy-dev] tool_dependencies.xml Environmental Variable Question

2014-03-25 Thread Dave Bouvier 

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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Re: [galaxy-dev] tool_dependencies.xml Environmental Variable Question

2014-03-24 Thread Greg Von Kuster 
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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