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cluster access

Matthias Bernt
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,
[hidden email], 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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Re: cluster access

Peter Cock
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
[hidden email] email aliases just for this.

Peter

On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <[hidden email]> 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,
> [hidden email], 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/
___________________________________________________________
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/
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Re: cluster access

Matthias Bernt
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
> [hidden email] email aliases just for this.
>
> Peter
>
> On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <[hidden email]> 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,
>> [hidden email], 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,
[hidden email], 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/

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Re: cluster access

Peter Cock
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
[hidden email] 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 <[hidden email]> 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
>> [hidden email] email aliases just for this.
>>
>> Peter
>>
>> On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <[hidden email]> 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,
>>> [hidden email], 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,
> [hidden email], 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/
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