Björn,

I have galaxy-dist. Was it the right choice?

Here is what I did. I copied your "tool_dependencies.xml" into my project (s_mart, in the test Tool Shed), and I created a testing XML file, which uses your dependencies:
---
<tool id="test" name="test">
        <description>This is a test.</description>
    <requirements>
        <requirement type="set_environment">PYTHONPATH</requirement>
        <requirement type="set_environment">PATH</requirement>
    </requirements>
        <requirement type="package" version="1.7.1">numpy</requirement>
<command>env > $outputFile; python -c "import numpy" >> $outputFile</command>
        <outputs>
<data name="outputFile" format="txt" label="output test file"/>
        </outputs>
    <help>This is a test.</help>
</tool>
---
I uninstall and reinstall the package, then run the test. Numpy seems fine (I got no complain), but PYTHONPATH and PATH are not updated.

I change "append_to" and "prepend_to" to "set_to" in the "tool_dependencies.xml". I unstall/reinstall my package... the variable dependencies have disappeared! When I run the test, the environment variables are left unchanged.

It seems now that Galaxy may have some problems with the reinstall. I tried to totally install my package, but Galaxy remembers having seen it and reinstalls it instead of a fresh install.

Could this be the source of the problem?

Matthias.


On Wed, 24 Apr 2013, Björn Grüning wrote:

Hi Matthias,

Sure,

This is the least I can do. However, I do not know how to install a
package from a simple XML, and without Tool Shed installed repository.

it's documented here:
http://wiki.galaxyproject.org/Tool%
20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance

I will check that.
I have downloaded Galaxy for installation less than a week ago.

Have you downloaded galaxy-dist or galaxy-central?

Cheers,
Bjoern

Matthias.


On Wed, 24 Apr 2013, Björn Grüning wrote:

Hi Matthias,

do you use the toolshed or the testtoolshed?
Can you please test the following repo and install:

testtoolshed.g2.bx.psu.edu/repos/bgruening/package_numpy_1_7

It also contains append_to and works for me. Also which version of
galaxy do you use?

Thanks!
Bjoern

Dear everyone,

I finally got the answer. The "append_to" does not seem do work in the
"tool_dependencies.xml":

---
<environment_variable name="PYTHONPATH"
action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable>
---
does not insert anything, while:
---
<environment_variable name="PYTHONPATH"
action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
---
updates the correct "env.sh" and "INSTALLATION.log" files.

Weird.

Many thanks for your help.

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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--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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