Re: [galaxy-dev] init scripts version 16.01
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
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
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
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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participants (3)
-
Eric Kuyt -
Marius van den Beek -
Peter Cock