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
# outputs to a directory for collection by Galaxy when the job is
# Previously, this directory was new_file_path, but using one global
# can cause performance problems, so using job_working_directory ('.'
# when a job is run) is encouraged. By default, both are checked to
# 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,
On Sat, Nov 16, 2013 at 6:19 AM, Nikhil Joshi <najoshi(a)ucdavis.edu> wrote:
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
UC Davis Bioinformatics Core
najoshi -at- ucdavis -dot- edu
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