Many thanks!
However, how matter how hard I try, I cannot see anything in this
directory.
I will investigate that.
À bientôt,
Matthias.
On Tue, 23 Apr 2013, Björn Grüning wrote:
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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