job_working / tmp folders

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job_working / tmp folders

Shrum, Donald C

I changed the values for new_file_path and job_working_directory in my config file.

 

After restarting galaxy I’m finding some of the tools still reference the old path which no longer exists.  Do these end up hard coded in some place… I haven’t done a find + grep to go looking yet but that may be the next step…

 

Thanks for any help

--Don

FSU Research Computing Center


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Re: job_working / tmp folders

John Chilton-4
I am not aware of any other way new_file_path is accessed. Is it old
jobs that were queued up prior to the switch? I think
job_working_directory might actually be affected by the settings in
your object store configuration. Have you configured an object store?

In either case - knowing the specific tools to look at that are still
referencing these old files might really help diagnose the problem.

Hope this helps.
-John

On Thu, Oct 30, 2014 at 1:56 PM, Shrum, Donald C <[hidden email]> wrote:

> I changed the values for new_file_path and job_working_directory in my
> config file.
>
>
>
> After restarting galaxy I’m finding some of the tools still reference the
> old path which no longer exists.  Do these end up hard coded in some place…
> I haven’t done a find + grep to go looking yet but that may be the next
> step…
>
>
>
> Thanks for any help
>
> --Don
>
> FSU Research Computing Center
>
>
> ___________________________________________________________
> 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
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Re: job_working / tmp folders

Shrum, Donald C
Thanks for the reply John,

It turns out my problem was with the drama conf file (forgot about that one) and I'm just posting this reply on the off change google leads someone else to the solution :)

-bash-4.1$ more /opt/pbs-drmaa/etc/pbs_drmaa.conf
user_state_dir: /panfs/storage.local/galaxy-data/tmp/.drmaa



-----Original Message-----
From: John Chilton [mailto:[hidden email]]
Sent: Sunday, November 02, 2014 5:20 PM
To: Shrum, Donald C
Cc: [hidden email]
Subject: Re: [galaxy-dev] job_working / tmp folders

I am not aware of any other way new_file_path is accessed. Is it old jobs that were queued up prior to the switch? I think job_working_directory might actually be affected by the settings in your object store configuration. Have you configured an object store?

In either case - knowing the specific tools to look at that are still referencing these old files might really help diagnose the problem.

Hope this helps.
-John

On Thu, Oct 30, 2014 at 1:56 PM, Shrum, Donald C <[hidden email]> wrote:

> I changed the values for new_file_path and job_working_directory in my
> config file.
>
>
>
> After restarting galaxy I’m finding some of the tools still reference
> the old path which no longer exists.  Do these end up hard coded in
> some place… I haven’t done a find + grep to go looking yet but that
> may be the next step…
>
>
>
> Thanks for any help
>
> --Don
>
> FSU Research Computing Center
>
>
> ___________________________________________________________
> 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/