job_conf.xml and nativespecification

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job_conf.xml and nativespecification

Laure QUINTRIC
Hi galaxy users,

while using galaxy with drmaa and real user on drm system, I would like
to know if there's a way to set the variable PBS_O_LOGNAME to the real
user name in the job_conf.xml :

<param id="nativeSpecification">-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q
test -l mem=100gb </param>

Thank you,

Laure

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Re: job_conf.xml and nativespecification

Björn Grüning-3
Hi Laure,

a hacky way it to use dynamic job destinations:

https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

You can get the username via python and change "nativeSpecification" on
demand.

Hope this helps,
Bjoern

Am 14.09.2016 um 17:07 schrieb Laure QUINTRIC:

> Hi galaxy users,
>
> while using galaxy with drmaa and real user on drm system, I would like
> to know if there's a way to set the variable PBS_O_LOGNAME to the real
> user name in the job_conf.xml :
>
> <param id="nativeSpecification">-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q
> test -l mem=100gb </param>
>
> Thank you,
>
> Laure
>
> ___________________________________________________________
> 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/mailinglists/
___________________________________________________________
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/mailinglists/