Problem displaying data on UCSC Cell Browser

I have a problem to display data on UCSC Cell Browser. I 'm trying to run Atlas-Seurat-CellBrowser workflow (GitHub - ebi-gene-expression-group/container-galaxy-sc-tertiary: Galaxy container for single cell RNA-Seq tertiary analysis tools) on my own local Galaxy (v19.05) and get html format data for UCSC Cell Browser. When I click the “View Data” icon of the result, UCSC Cell browser starts but the result cannot be displayed even though I click “Open” button. I also uploaded the result on Human Cell Atlas Galaxy ( and found again it wasn’t displayed.

I tested on other versions local Galaxy and figure out t works on Galaxy version 18.05 and 19.01 but doesn’t work on 19.05 and 19.09. Also I tried other clients, Mac/Windows, Safari/Firefox/Chrome only to get same behaviour.

Anyone have the same problem? What might be wrong?

Thank you.

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Hey Yukie,

Did you ever find a solution? I’d be very interested to know how your experience has been with using the Seurat object after the Export2CellBrowser Step, with the newer versions of the UCSC browser tools like (0.7.10+galaxy0, +18.01).


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@tshum @yukieymd

Data in HTML format cannot be uploaded at public Galaxy servers intact.

Any data in HTML format that was created at any particular Galaxy server has a specific flag that allows it to be displayed at that server when using the “view data” icon (“eye”).

Both are for security reasons at public Galaxy servers, including

I’m not sure about all the details at You could contact them and ask a question, or you can try to figure out the usage first. You might just need to set the data to be in a “shared” state in Galaxy. Or, maybe download the data into a local file and try to load it that way. They do offer a version that can be set up locally – similar to how you set up Galaxy locally – and I would expect that permission configurations could be customized by the administrator (you).


  1. HTML data is blocked by default (Upload and display). How any particular private Galaxy server handles HTML format is configurable by the server administrators. Decisions depend on if the server is publically accessible, has moderated access/account creation methods, etc.
  2. Data needs to be publically accessible (on a server hosted publically) and have the privacy preferences set as “shared” to move data from Galaxy to a different public web service. Plus, any service in the EU will be following GDPR compliance strictly.
  3. That service may be another Galaxy server or it may be a third-party application.
  4. Data in a shared state is still somewhat “private” for many use-cases – but this is not the same as encrypted/secure data transfer. Data have distinct URLs. When those data URLs are in a shared state, someone would have to correctly “guess” the data URLs with an open sharing access set in order to gain access.
  5. Any work that needs to be completely secure/protected should not be created or uploaded to public web services – Galaxy or otherwise.
  6. There are many ways to use Galaxy for sensitive data with security/privacy requirements (example: personally identifiable human biological data). These deployments are usually behind a firewall and are not publicly exposed.

Practical help for end-users:

Administrative topics:

Hope that helps!

Hi Thomas,

Sorry for my late reply. The newer versions seem to work fine!


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