Hi George,

on our instance I have noticed that the tmp (new_file_path) was taking up quite some space and files were only deletable after restarting the web / uwsgi process.

FYI a while ago I wrote this script which should ease the cronjob setup a bit (does not cleanup tmp though): https://github.com/galaxyproject/galaxy/blob/dev/scripts/maintenance.sh

Cheers, Jelle

On Tue, Oct 30, 2018 at 5:04 AM George Weingart george.weingart@gmail.com wrote:

Hello,

We are incurring a problem with cleanup.py:

We have already run two cycles of cleanup.py (1-6) with a cut off of 30 days, we see in the logs that many datasets are deleted, but when we do df -kh to check the file system, we see creeping up utilization of space - no relinquishing of any space.

We are running in a docker environment and our cleanup job looks as follows: ================================================================

#!/bin/bash

export GALAXY_VIRTUAL_ENV=/galaxy_venv

source $GALAXY_VIRTUAL_ENV/bin/activate

export script="/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py"

export config="/etc/galaxy/galaxy.ini"

export logdir="/export/galaxy-central/logs"

export days=30

export num=$1

nohup $script $config -d $days -$num -r -f >> $logdir/cleanup$num.log &

================================================================

and we run it with ./run_cleanup.sh 1

or 2, 3 etc.

Any ideas ?

Thanks!

George Weingart PhD

Huttenhower Lab

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