Well, here's one config that should work.  I'll guess that you have the same 
cleanup_datasets/ folder contents as I do so... having logged in as user that 
galaxy runs under, doing a 

crontab -e 

on command line should get you crontab settings for that user.  I have an older 
longer line that handles daily cleanup...

0 0 * * * sh /[path to your 
galaxy]/galaxy-dist/scripts/cleanup_datasets/delete_userless_histories.sh; sh 

or a more abbreviated version:

@daily cd /[path to another galaxy 
instance]/galaxy-dist/scripts/cleanup_datasets && sh 
delete_userless_histories.sh && sh purge_histories.sh && sh purge_libraries.sh 
&& sh purge_folders.sh && sh delete_datasets.sh && sh purge_datasets.sh

Hopefully that works for you...

Message: 4
Date: Wed, 19 Nov 2014 22:14:19 +0000
From: James Mullan <jamespamul...@gmail.com>
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] How to get cleanup script to run in cron job ?
Content-Type: text/plain; charset="utf-8"

         I am trying to figure out how to run the cleanup scripts in a cron
job. The below works on command line:
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