Tophat not working??? - Deprecated tool, use HISAT2 instead

Ran Tophat 5X on same data set that worked 2 days ago… Is Tophat down? I have deadlines to meet…

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hi @rpotens007

Are you working at Galaxy Main

If yes, then there are known issues with some mapping jobs. Choosing a specific cluster to run the jobs on will help until the issues are fully resolved.

Ticket about the problem (will close out once fixed):

Workaround with details about how to target the proper cluster is linked from that ticket above, but here is the post directly: HISAT2 Not working

This is a priority correction and we expect a full resolution soon.

Update: Fixed

Note to all end users running mapping: Using all defaults for the “Job Resources” parameter is a good choice now again. No need to target a particular cluster anymore. Allowing Galaxy to choose the target cluster based on the currently available resources, at the time of job submission, is the fastest way to run tools.


Hi Jennifer,

Thank you for addressing the mapping issue. Looks like it is working fine.


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Super, thanks for letting us know :slight_smile:

I am unable to get TOPHAT to work the past several days. It churns away and finally i get an error message. Is it still supported?

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Tophat has been deprecated for many years now. It is not maintained anymore and could present with issues at any time. We were able to get a workaround before, but that may no longer be possible, or if fixed, it won’t be soon.

Everyone needs to migrate away from using Tophat. HISAT2 is the replacement.

Prior Q&A that covers alternatives: