tool_dependencies.xml Environmental Variable Question
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 mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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 <mepcotterell@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 mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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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 mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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participants (3)
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Dave Bouvier -
Greg Von Kuster -
Michael E. Cotterell