Hi Matthias,

> Dear Björn,
> Maybe the problem is here. I cannot find neither "tool_deps", nor 
> "env.sh".
> The install is fresh from yesterday... I should check why I did not 
> generate these files.
> By the way, if "env.sh" is sourced right before my script, I should see 
> the updated PYTHONPATH in the result of the command "env > $outputFile", 
> no?

Yes :)
The tool_deps directory is set in universe_wsgi.ini under:
tool_dependency_dir = ./tool_deps/

Ciao,
Bjoern

> Many thanks,
> Matthias.
> 
> 
> On Tue, 23 Apr 2013, Björn Grüning wrote:
> 
> > 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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> >
> >
> >


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