Hi Nikhil,

  Many things other than this variable number of outputs mechanism use
the new_file_path and Galaxy doesn't really "manage"/clean anything
put in that directory - it should be thought of as temp space (like
/tmp) but that should be shared over the cluster (if you have one).
For this reason, I guess ideally one would setup a cron job to clean
out files older than a few weeks out of this directory - that said we
never did this when I was working at MSI where we had a fairly large
Galaxy instance. That directory would grow to a few hundred gigabytes
- but on a multi-petabyte file system automating the cleanup on that
never seemed like a priority.

  Looking at this comment it universe_wsgi.ini though, I am think it
would be better to just create these files in the jobs working
directory - which will get cleaned up by Galaxy (unless you set
cleanup_job in universe_wsgi.ini to never).

# Tools with a number of outputs not known until runtime can write
these
# outputs to a directory for collection by Galaxy when the job is
done.
# Previously, this directory was new_file_path, but using one global
directory
# can cause performance problems, so using job_working_directory ('.'
or cwd
# when a job is run) is encouraged.  By default, both are checked to
avoid
# breaking existing tools.
#collect_outputs_from = new_file_path,job_working_directory

  I will try to find some time to test this out and update the
documentation on the wiki.

Thanks for the post,
-John

On Sat, Nov 16, 2013 at 6:19 AM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
> Hi all,
>
> So I am using this documentation to create a tool that has a variable number
> of output files based upon the input file.  I have gotten it to work,
> however, the intermediate files which I create in the $__new_file_path__
> directory (which are then copied into the database as history files) are not
> being deleted upon tool completion.  Is there a way to get galaxy to
> automatically delete these files, or is there some programmatic way to do
> it?
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
>
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