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,
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, 20
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 var
