In my galaxy there are 3 users with 474, 312 and 0 gigabytes of used space as galaxy says. However the database actually uses 1.2 TB of disk space. I ran cleanup scripts Cleaning up Dataset Objects but they freed exactly 0 bytes.
What else my database contains that is not shown and can not be deleted by scripts? Can i delete it in some other way?
Hi @wormball, are you running Postgresql as the database? If so then you may need to run VACUUM FULL. You will need to stop Galaxy for this work though. PostgreSQL: Documentation: 12: VACUUM
So the difference between 1.2 and what you see as Galaxy datasets is exactly the size of the /tmp folder. You can clean it up periodically with something like tmpreaper. Thanks @ggbio for identifying this.
I reviewed our workflow, and it turned out that it were poorly written custom tool xmls that left tons of garbage behind them. Now i had fixed them, and galaxy is innocent.