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 <najoshi@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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