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:

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#!/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 &

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and we run it with ./run_cleanup.sh 1

or 2, 3 etc.

Any ideas ?

Thanks!

George Weingart PhD

Huttenhower Lab

Harvard School of Public Health