I am writing to request your assistance in recovering a dataset that was recently purged from my Galaxy history. Unfortunately, I was unable to retrieve it through the user interface, and I am aware that purged datasets are typically irrecoverable.
However, I wanted to inquire if there are any backup systems or alternative options that could help restore this dataset.
Purging a dataset is a permanent action. The space recovered is reused.
The good news is that the purged dataset itself will stay in your history for a few days. That means you can use the rerun icon to bring up the tool form again with all the original settings. Maybe helps to reproduce what was lost?
Thank you for your precious comment, I appreciate.
My history does not contain the purged dataset any longer so I am not able to rerun, I have tried that. Would you recommend any other action that could help me?
First, I’m really sorry that you lost your work. Everyone knows exactly what you are feeling! Ug.
I don’t have other advice for what is already gone, but going forward there are a few things you could consider adding in to your own personal analysis “flow”. (this advice comes from decades of experience, and paranoia!)
Keep a log of what you are doing, as you are doing it.
This can be tedious but has saved me. One of the reasons I first noticed and really liked Galaxy is that the application made this much faster and easier to do. (anyone who has manually labeled files with progressively longer “informative” names, or sorted data into yet more nested directories, or had to remember to write into a README log… knows what I’m talking about).
So – what is that Galaxy “keeping a log” strategy?
Extract workflows from the history. These don’t have to be perfect – they can be just for you, consume zero quota space, and never expire. Think of it as a permanent log of exactly what happened, with an automatic timestamp. You can add notes and such, or just grab-and-go.
Export a history to a file, and download it. Why? To make sure that you control any data that is critically important to you. (this advice applies to any public web service … email, etc.). Put your downloads on a stick, or a paid storage space somewhere that does have backup capabilities.
Create a copy of a history. I do this all the time. Then clean things up once I’m done (after I have a decent workflow “log”, and after I have a downloaded “exported file”). Remember: exact copies of data in your own account do not consume any extra quota space – so this is “free”.
Put your final cleaned up important datasets into an archived history. This prevents unintentional changes. This will count toward your quota space, but that’s just how public resources work (practical data storage limits). I tend to pair an archived history with a workflow – then name both the same, and make sure the same name is on my downloaded versions of both – but how much you want to invest in this layered approach is your decision.