Hi Marius,

Now I ran in to some problems.

When trying to change metadata of a file, the python path changes (these tools run using drmaa) to the normal system version. Here tools are ending in error becaus sqlalchemy.orm cannot be found. I can ofcourse install sqlarchemy-python systemwide. But this woudn't make me very happy.

in File: <galaxy>/lib/galaxy_ext/metadata/set_metadata.py a sys.path.insert to .venv/lib should be added. I don't know what the right plcae for this is.

Do you hava any better ideas for this matter?

Eric

On 8 April 2016 at 16:15, Eric Kuyt eric.kuijt@wur.nl wrote:

​Thanks, works like a charm!​ Clean easy fix, Now why I couldn't come up with this myself.

On 2 April 2016 at 11:49, Marius van den Beek m.vandenbeek@gmail.com wrote:

...

ld have been mentioned with the release notes. I didn't test this, but it might be sufficient to replace PYTHON="/usr/bin/python" with PYTHON="<path/to/venv/bin/python>". If that is sufficient for you, let us know and we will update the wiki and adjust the script in

-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl

We had something similar breaking when using run-as-real-user, where config/galaxy.ini setting external_chown_script which defaults to scripts/external_chown_script.py was being run on the cluster nodes using the system default Python.

Here we created a wrapper shell script which invoked the Python script via the correct Python 2.7 used by the main Galaxy instance:

external_chown_script = scripts/external_chown_script.sh

The symptoms were the same though - Galaxy's dependencies could not be found.

Peter

On Mon, Apr 11, 2016 at 1:30 PM, Marius van den Beek m.vandenbeek@gmail.com wrote:

Hi Eric,

Take a look at this https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#w... . I hope that should be sufficient.

Cheers, Marius

On 11 April 2016 at 14:25, Eric Kuyt eric.kuijt@wur.nl wrote:

...

Hi Marius,

Now I ran in to some problems.

When trying to change metadata of a file, the python path changes (these tools run using drmaa) to the normal system version. Here tools are ending in error becaus sqlalchemy.orm cannot be found. I can ofcourse install sqlarchemy-python systemwide. But this woudn't make me very happy.

in File: <galaxy>/lib/galaxy_ext/metadata/set_metadata.py a sys.path.insert to .venv/lib should be added. I don't know what the right plcae for this is.

Do you hava any better ideas for this matter?

Eric

On 8 April 2016 at 16:15, Eric Kuyt eric.kuijt@wur.nl wrote:

...

Thanks, works like a charm! Clean easy fix, Now why I couldn't come up with this myself.

On 2 April 2016 at 11:49, Marius van den Beek m.vandenbeek@gmail.com wrote:

...

ld have been mentioned with the release notes. I didn't test this, but it might be sufficient to replace PYTHON="/usr/bin/python" with PYTHON="<path/to/venv/bin/python>". If that is sufficient for you, let us know and we will update the wiki and adjust the script in

-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl

-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl

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