As someone without access to a local server, I am very grateful to be able to use this free server for my bulk RNA-seq analysis. About two weeks ago, I uploaded my raw data and was able to complete part of the preprocessing successfully. However, when I logged in again this week to review my previous data, I found that all of the files had been deleted. I am now trying to re-upload one sample as a test, but although the upload reaches 100%, a red warning message appears, and the file is not being saved in the history. Could you please advise me on how to resolve this issue?
Welcome @E11
Which public Galaxy server are you working at? Find the URL at the top of your browser window. You can post that back here in your reply. I can see your brand new account at UseGalaxy.org, and there is only one history and two dataset. Were working at a different server before, or you are also working at UseGalaxy.org?
How data is stored at public Galaxy servers
Data included in your permanent or temporary storage choice is saved differently, and each server will have a different data retention policy.
Details will be included on the server under User → Preferences → Manage Your Preferred Galaxy Storage. You can navigate your data under User → Preferences → Storage Dashboard, or click on the database icon at the top of history views. The server may also have more details linked under the 
icon at the top.
Data in a temporary storage will expire and be removed, and permanent data is retained until you remove it. Any data that you want to move around between storage locations can be adjusted on the dataset’s Details page.
- A guide that links to some of the UseGalaxy per-server documentation → How to access your Self Serve extended data storage at UseGalaxy servers!
- We have discussion at storage-dashboard. See topics like → Navigating your data storage: existing data, new data, and different storage space options with screenshots!
Datasets in temporary storage have a countdown timer exposed.
One strategy is to upload or create data into the storage you want it to be. You can also move data between storage locations by using the i-info icon → Dataset Details → Dataset Storage.
Your questions
With that context, for this
One of these is likely going on:
- data was originally loaded into a temporary storage space
- you might be logging into a different server that you originally worked at? (these are easy to mix up!).
- the data is only deleted and not purged (permanently deleted). This case means the data could be recoverable by undeleting.
How to find and undelete datasets
How to find and undelete histories
Two weeks is shorter than the data expiration period at the larger UseGalaxy servers – this is why I was asking about which server you are working at. We can help to find the storage documentation so you can learn how to manage your data there. Galaxy also does not delete histories, only datasets, so this part is a bit confusing, and more details will help us to help you.
Then for
This likely means that the current storage is filled up. You won’t be able to load more data or run tools until there is free space to write more data. I would suggest looking under your User → Preferences → Storage Dashboard to review.
My guesses are
- the original data is still there, in a deleted state, and still counting towards quota.
- or, you are now loading data in the smaller permanent space (smaller) when you previously were using the temporary space (larger!), and your files are large enough to require the use of the temporary space.
Review
Please give this a review! The server URL will help. You can also post some screenshots of the review areas I mentioned, and we can help to interpret them.
Let’s start there, and we can sort this out so that nothing unexpected happens again! 