We've been running a private GVL/Galaxy instance for a number of weeks with 2-3 users. All was well until recently. We have set up 1.5 TB elastic block storage to service our galaxy instance, and we recently noticed it contains 0.6 TB of data, despite the fact that we've confirmed that everyone has permanently deleted and purged all unwanted histories and files. Disk use via the http://XX.XXX.X.XX/reports/ interface provided through GVL/Cloudman shows that only 98.8 GB in use and no jobs currently running. After some sleuthing, I tracked down the offending space-hogging files to the /mnt/galaxy/tmp folder. They are a bunch of "url_pasted..." files left-over from a number file uploads from Amazon S3 buckets into our Galaxy instance. Those files were utilized and deleted (or so we thought) after uploading; however, they seem to still be around. I've tried directly deleting them both via "ssh-ing" into our galaxy instance or looking at the directory through a Lubuntu desktop interface also provided through GVL/Cloudman and throwing them in the trash, but in both cases, I'm prevented from deleting the offending files, as "access permission is denied". I'm assuming I need root access, but I can't seem to get this. Are there other ways to remove these files? Why are they otherwise "invisible" to us despite our Admin access?
To delete the files you just need to become
galaxy system user with
sudo su galaxy on the command prompt and then navigate your way to the directory to delete the leftover files. BTW, Galaxy occasionally leaves such files behind in case of a failed upload.