job_working_directory

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job_working_directory

Shrum, Donald C
I'd like to set the job_working_directory to the user's home directory.

I'm using an apache proxy with ldap authentication.  I'm assuming I need to strip the remote_user_maildomain off the user name to do something like...

job_working_directory = ~%user/galaxy_working_directory

Is this possible?


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Re: job_working_directory

John Chilton-4
There is certainly no flag in Galaxy to allow this.

Even if you tried to hack it in - there would be some problems. Galaxy
writes out some files to that working directory before running the job
- so there would need to be more chown-ing and stuff happening at the
beginning of the job - probably before it even got to the runner
component. If Galaxy could assume these directories already existed
and didn't need to run the jobs as the real user - this would be a lot
easier (not easy, just easier) to hack into Galaxy - but I assume you
want to run these jobs as the real user.

I've created a Trello card for this request: https://trello.com/c/n1UitJTb.

Sorry I don't have better news.

-John

On Wed, Jun 25, 2014 at 3:51 PM, Shrum, Donald C <[hidden email]> wrote:

> I'd like to set the job_working_directory to the user's home directory.
>
> I'm using an apache proxy with ldap authentication.  I'm assuming I need to strip the remote_user_maildomain off the user name to do something like...
>
> job_working_directory = ~%user/galaxy_working_directory
>
> Is this possible?
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/