Missing tools from the ASAIM MT workflow

usegalaxy.eu support
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1

Hi everyone,
I am currently analyzing some microbiome data using the ASaiM-MT workflow. However, the workflow keeps running into errors. I thought I could work around this by running the tools manually, one by one, but several of the required tools are difficult to locate and i cant find them under tools. Is there a replacement or workaround for this?

Specifically, I am looking for a way to:

  1. Create a genus-level gene families file,

  2. Unpack pathway abundances to show which genes are included, and

  3. Group abundances of UniRef50 gene families (from HUMAnN2 output) to Gene Ontology (GO) slim terms.

Thanks a lot for your help!:folded_hands:

2

Hi @Sabsida

Do you want to troubleshoot these errors? Running the tool directly and in a workflow will yield the same result. Then, as needed, you are rerun tools that a workflow originally ran, replace the results, or go in and modify the workflow. We can help with all of that.

And, to confirm, you are running these at UseGalaxy.eu? You could move over to https://metagenomics.usegalaxy.eu/ instead. Your account is the same as at the primary EU server. The main difference is a simplified tool panel and a homepage with domain specific resources.

I do see at least one tool that is included in the workflow that is not exposed directly in the tool panel. I am not sure if that was intentional or not.

Let’s ask the MicroGalaxy team what they think at their chat for feedback. They will probably reply here but feel free to joint the chat too! (either through this link, or through the link at the top of the tutorial home page here). :microbe: You're invited to talk on Matrix

And finally, as a cross check to see how this is working today, I started up the tutorial data through the current workflow in this shared history.

Let’s start there and we can follow up! :slight_smile: