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.
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