Snippy tool bug?

Can someone tell me if there is a bug in the Snippy tool?

Hi @Boet

There aren’t any open issues for the current versions hosted at the UseGalaxy.* servers: Issues · galaxyproject/tools-iuc · GitHub


If you need technical help, please post back the exact tool version/source, describe where you are working (public server URL or private Galaxy type/version), and please note if there is anything special about the inputs or parameters.

Let’s start there, thanks!

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i use this version


T, S. (2015). snippy: fast bacterial variant calling from NGS reads. GitHub - tseemann/snippy: Rapid haploid variant calling and core genome alignment


  • snippy (Version 3.2)


We use this for education for some years now but the datasets do not work anymore in the tool. We did not change anything. Thanks for the help.

we use this tutorial.

Ok, thanks for the extra information.

Was your problem with the copy/paste function for the “Get-Data” step? There was an extra leading space on each of the URL lines. I fixed that here and it is pending a merge: Fix FTP links microbial-variants by jennaj · Pull Request #3664 · galaxyproject/training-material · GitHub

What you can do for now: remove the extra leading space for each URL before submitting to the Upload tool.

If that was not the problem, please generate a share link to the history that contains the inputs and outputs and post that back. Please do not delete the errors.

I’m also running a test using the tutorial data and workflow at the server – still processing and will post that back once done.

That went quick! Snippy step completed successfully. The data, history, and workflow below all exactly match the tutorial’s content – with the exception of the leading spaces removed from the data URLs during the initial Upload step. I’ll leave this shared as a reference and anyone can view or import.

History Galaxy | Europe | Accessible History | test gtn microbial-variants
Workflow Galaxy | Europe | Accessible Workflow | Microbial Variant Calling (imported from URL)