Resolved: Tools are missing in my account (main server)

A few hours ago the website wasn’t loading, and about an hour later when it came back online, certain tools were missing like featureCounts and Download and Extract Reads in FASTQ format from NCBI SRA. Its weird because I could not find them even when using the search bar, but if I clicked on a dataset from my history that used those tools, and select rerun, the tool is there and seems to work just fine, although the fastq-dump failed the first time, it seems to be working now. Is everyone having this issue?
I have been downloading a lot of fastq files, aligning to genome with hisat2 and doing feature counts, and then deleting the fastq files and bam files due to storage quuota, so I feel like someone wants me to stop using resources and just removed the tools from my account.

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Also, my disk quota is not refreshing after deleting and purging some stuff (its been a few hours since doing this). I am at 51% and I should be closer to 25%, it usually updates pretty quickly after purging deleted datasets.

The same thing has happened to me where most of the tools are missing as of this morning after receiving the error message that Galaxy is unable to start. I cleared my history as well but did not see any difference.

Hi @Ian_Mersich and @Mitch_Godin

Yes, I noticed the same thing (was searching with keywords). We are updating the server. More feedback soon!

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Hi! Are there any updates on when these tools will be available again?


Hi - Again any update when the tools will be back?

Hi @megi

We are still waiting on a change to be applied but by the end of the week for sure.

The tools are still on the server, just not in the tool panel. That means (existing) workflows and reruns still function fine. Extracting workflows also functions. But new tool searches fail.

For anyone in a rush who doesn’t have a workflow: try at EU or AU instead.

Updates will continue to post here until resolved. Thanks!

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This issue has been fixed and deployed on Thank you for reporting it and for your patience. Cheers.