How set the working and temp directories in external drive

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How set the working and temp directories in external drive

jvdelarosa
Hi,

now I am trying to set the working and temp directories of Galaxy enviroment in a external drive, but I do not know how to do this task. I know that universe_wgsi.ini file has a section called Files and directories, with diferent options like job_working_directory, collect_outputs_from, file_path and new_file_path. However, I do not know if these are the options to be set or if there are other options. I also do not know how to set these options. Can anybody help me or point me to a tutorial?

Thanks

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Re: How set the working and temp directories in external drive

John Chilton-4
So you want temp directories and working directories to sit on the
external drive but not Galaxy's files:

Lets say this external disk is mounted as /mnt/gxwork. I would create
two directories under that maybe /mnt/gxwork/tmp and
/mnt/gxwork/working.

Setting the working directory is the easier part - you just need to set

job_working_directory = /mnt/gxwork/working

Ideally - where Galaxy tools write temporary files is handled outside
of Galaxy - so if you could mount /tmp using that /mnt/gxwork/tmp
directory it would be best. This isn't always realistic though. The
alternative is to make sure all jobs run with TMP, TEMP, and TMPDIR
environment variables set to that directory. There are a myriad of
ways to do this that are going to depend on your configuration. In
most cases - it is probably best to just place these definitions in
your Galaxy users .bashrc file maybe - if you really want Galaxy to
handle this I think you can setup an environment file and point the
environment_setup_file option at it.

So create a galaxy_job_env file with following contents:

export TMP=/mnt/gxwork/tmp
export TEMP=/mnt/gxwork/tmp
export TMPDIR=/mnt/gxwork/tmp

and then set environment_setup_file in Galaxy's universe_wsgi.ini to
point at it.

Some older tools will use - new_file_path in universe_wsgi.ini for
temporary directories. So I would also point this at that
/mnt/gxwork/working.

Hopefully this helps.

-John

On Wed, Aug 13, 2014 at 12:08 PM, Juan Vladimir de la Rosa Medina
<[hidden email]> wrote:

> Hi,
>
> now I am trying to set the working and temp directories of Galaxy enviroment
> in a external drive, but I do not know how to do this task. I know that
> universe_wgsi.ini file has a section called Files and directories, with
> diferent options like job_working_directory, collect_outputs_from, file_path
> and new_file_path. However, I do not know if these are the options to be set
> or if there are other options. I also do not know how to set these options.
> Can anybody help me or point me to a tutorial?
>
> Thanks
>
> ___________________________________________________________
> 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/
___________________________________________________________
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