Dear list,
I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login).
The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior?
Thanks a lot.
Cheers, Matthias
This may depend on the cluster setup, and how Galaxy accesses it. What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup username@example.org email aliases just for this.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login).
The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior?
Thanks a lot.
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
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Hi,
sorry, I forgot this central piece of information: We also use Univa Grid Engine.
What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this.
Best, Matthias
On 10.04.2017 16:39, Peter Cock wrote:
This may depend on the cluster setup, and how Galaxy accesses it. What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup username@example.org email aliases just for this.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login).
The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior?
Thanks a lot.
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
That's interesting. I didn't set this up on our system, but if the LDAP can tell Galaxy the real username, maybe we can avoid having to setup username@example.org aliases and insisting our users do that for logging into Galaxy.
Hopefully some other SGE users can comment on how they got the run-as-user system working for them?
Peter
On Mon, Apr 10, 2017 at 3:43 PM, Matthias Bernt m.bernt@ufz.de wrote:
Hi,
sorry, I forgot this central piece of information: We also use Univa Grid Engine.
What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this.
Best, Matthias
On 10.04.2017 16:39, Peter Cock wrote:
This may depend on the cluster setup, and how Galaxy accesses it. What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup username@example.org email aliases just for this.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login).
The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior?
Thanks a lot.
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
Dear list,
I had some time to dig into this.
Since this is a quite old thread here is a wrap up:
The problem was that galaxy uses the USER part of the email address (USER@DOMAIN) to determine the system user to submit jobs to a drmaa cluster (I need to submit jobs as real user). In my setting, where users login via LDAP, this does not work since the prefix of the email is not always the user name, but the actual user is stored in the galaxy data base (and awaited utilization :) ).
I found a way to let galaxy try both possibilities, and whatever of the two possibilities matches a real user is taken (prioritizing the email method for compatibility). I have created a pull request:
https://github.com/galaxyproject/galaxy/pull/4096
Cheers, Matthias
On 10.04.2017 17:03, Peter Cock wrote:
That's interesting. I didn't set this up on our system, but if the LDAP can tell Galaxy the real username, maybe we can avoid having to setup username@example.org aliases and insisting our users do that for logging into Galaxy.
Hopefully some other SGE users can comment on how they got the run-as-user system working for them?
Peter
On Mon, Apr 10, 2017 at 3:43 PM, Matthias Bernt m.bernt@ufz.de wrote:
Hi,
sorry, I forgot this central piece of information: We also use Univa Grid Engine.
What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this.
Best, Matthias
On 10.04.2017 16:39, Peter Cock wrote:
This may depend on the cluster setup, and how Galaxy accesses it. What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup username@example.org email aliases just for this.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login).
The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior?
Thanks a lot.
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
galaxy-dev@lists.galaxyproject.org
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Matthias Bernt -
Peter Cock