Hi Matthias, PYTHONPATH will not be changed globally. It's only changed during execution of your tool. Have a look under ./tool_deps/.../.../.../s_mart/ there is a file called env.sh with your PYTHONPATH. That file is executed before your command <command>env > $outputFile</command> is executed. Hope that helps, Bjoern
Dear everyone,
I have spent hours trying to set environment variable in Galaxy. I am managing the "s_mart" repos (you can check it if you wish), and I created the simple files "test.xml" which prints the environment variables: --- <tool id="test" name="test"> <description>This is a test.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command>env > $outputFile</command> <outputs> <data name="outputFile" format="txt" label="output test file"/> </outputs> <help>This is a test.</help> </tool> ---
and "tool_dependencies.xml", which appends something to the PYTHONPATH variable.: --- <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="PYTHONPATH" action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency> --- As you guess, I cannot see anything added in the PYTHONPATH variable. I have tried to append INSTALL_DIR and even "/tmp". None worked.
Do you have any suggestion for me?
Many thanks to you all,
Matthias. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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