Importing from USCS main table browser - invalid HTML content

[Tcomplex]

Hi, Trying to import datasets from UCSC Main Tables to Galaxy. Get error: “The uploaded file contains invalid HTML content.” Same results with any data type. Used to work fine in the past. Is there a known bug now?

[jennaj]

Hi @Tcomplex

Yes, the link sent from UCSC changed unexpectedly for all queries, and we are working with them to fix the problem.

This Q&A from earlier today has all the details. In short, download the output from the Table Browser to your computer, then upload it to Galaxy to get around the problem. The files themselves are not impacted, just the “handshake” URL between the two services.

@jennaj

The problem seems to be with how the data is moving into Galaxy. We’ll need to figure out why.

The file content itself is fine. I was able to download the file directly (instead of checking the “send to Galaxy” box), then upload the file to Galaxy. You can get a copy from my history.

How to:

1. Click on this shared history link to open it in a browser window Galaxy | Europe
2. Use the “Import” button found in the top left corner
3. Go into the User → Histories menu in the top masthead, and navigate to the imported history
4. Copy the dataset into your history. Copy a dataset between histories

Or, you can just work in the imported history. It is yours to work in, copy data out of, run more jobs in, then later even delete as you want :). Copies of histories are fully independent, so if anyone else runs into this problem before we can fix it, they can do the same when working with this tutorial, or can download/upload the particular file they need.

Update2: The issue has been reported to the UCSC team at their mailing list and is pending a correction. https://groups.google.com/a/soe.ucsc.edu/g/genome/c/-OLkG9MnwMk

[jennaj]

Update August 28 2025

The original issue was resolved some time ago, but for anyone running into the problem today, it appears to be back! We are investigating. The original work-around can be used.

Updates will post to → Bug: UCSC Main Table browser to Galaxy history · Issue #20833 · galaxyproject/galaxy · GitHub

cc @Galt_Barber I’m not sure if you follow this forum for updates, but in case you do .. what do you think? Would you like to comment at the Galaxy repo above or suggest who may be able to help? I tried a few different ways at the ORG (US) and EU servers, same result, so I think this is everywhere, and I don’t think it is known but please correct me. Thank you!

[jennaj]

Updates!

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