[galaxy-user] temporary files

[Nate Coraor]

Christopher Schroeder wrote:
> Dear all,
> 
> we extended the galaxy functionality with a couple of smaller custom
> scripts. Now we are in the need of some tmpFiles, since our data is
> getting bigger. As far as I understand galaxy by now there might be
> several options:
> 
> - job_working_directory (all "normal" files generated by the job,
> deleted upon completion of  job - safe?)
> - tmp-folder within the database folder (custom path in universe_wsgi.ini?)
> - system-tmp-folder (e.g. samtools-wraper -> only very limited space
> on this harddisk)
> 
> What is the best way to store temporary data in Galaxy (that can be
> deleted after job completion)?

Hi Chris,

It's really up to your personal preference.  In the past we've used all
three.  In general, if the filesystem your job_working_directory resides
in is suitable, it is probably the easiest choice since you get free
cleanup on job completion.

--nate

> 
> Thank you in advance for your help!
> Chris
> 
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/