QIIME2 version 2025.04 not working

usegalaxy.org support
,
1

Dear Galaxy staff,

I am trying to do a 16S amplicon analysis using QIIME2 on Galaxy following the instructions here: Moving Pictures tutorial 🎥 - Microbiome marker gene analysis with QIIME 2. Intriguingly, I found the latest version of QIIME2 installed on Galaxy (2025.4.0+q2galaxy.2025.4.0 on https://usegalaxy.org/) failed constantly, but the same analysis could be done using an earlier version (2024.10.0+q2galaxy.2024.10.0). The same is true for several other QIIME2 tools.

In addition, the tool “qiime2 composition da-barplot” is mentioned in the tutorial, but could not be found on Galaxy. There is an earlier discussion on it (da-barplot for Qiime2 visuaisation of ANCOM-BC), but it seems that the tool has not been installed yet.

Could you please take a look at these two issues? Thanks very much!

Best,
Xiaofan

2

Hi @Xiaofan_Zhou

Interesting issues – and we can try to resolve those here. I know that these wrappers have undergone some changes and updates. Maybe something is not configured correctly.

Questions so I can reproduce and get it reported as needed.

  1. For the tutorial – did you run that with the the tutorial data? Or does it work on the tutorial data, but later fail on full sized custom data? Would you please share the history so I can double check how I am translating the usage into Galaxy to trigger the error? I’m also curious about which server you are working at, but the shared history(ies) will include that.

  2. For the “qiime2 composition da-barplot” tool, I am looking at that right now. I’ll check if the wrapper is actually ready or not to be installed.

Let’s start there! :slight_smile: