Re: [galaxy-dev] cluster access

2017-05-22 Thread Matthias Bernt 

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
usern...@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  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
usern...@example.org email aliases just for this.

Peter

On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt  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.be...@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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--

---
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.be...@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
---



--

---
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.be...@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.

Re: [galaxy-dev] cluster access

2017-04-10 Thread 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
usern...@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  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
>> usern...@example.org email aliases just for this.
>>
>> Peter
>>
>> On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt  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.be...@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.be...@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:
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Re: [galaxy-dev] cluster access

2017-04-10 Thread 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
usern...@example.org email aliases just for this.

Peter

On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt  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.be...@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.be...@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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Description: S/MIME Cryptographic Signature
___
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/

Re: [galaxy-dev] cluster access

2017-04-10 Thread 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
usern...@example.org email aliases just for this.

Peter

On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt  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.be...@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/
___
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/

[galaxy-dev] cluster access

2017-04-10 Thread 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,
m.be...@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
---



smime.p7s
Description: S/MIME Cryptographic Signature
___
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:
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