QIIME 2 installed in Galaxy, but tools not appearing in the left panel (Mac mini M4 & Ubuntu)

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Welcome @HKadokawa

Thanks for posting all the details! Very helpful. It sounds like you have done quite a bit of troubleshooting, and I think I spot the issue. The older integrated_tool_panel.xml is likely missing the Qiime2 package or has a typo or similar.

My guess is that the default file that you loaded is not a match for your currently installed tools or has some typo. It is usually best to allow Galaxy to create this file upon startup, then to go in and customize it for yourself or, better, to use a tool_conf_labels.xml file to further manage the automation.

Layout

The various tool configuration files described in the previous section are all used to load tool panel items (tools, sections, labels, and workflows). A file named integrated_tool_panel.xml defines the arrangement for displaying these loaded items in your Galaxy tool panel. If this file does not exist in your Galaxy installation directory, it will be automatically created and populated when you start your Galaxy server. It is initially populated based on the order in which the tool panel items are loaded. The items are loaded as each tool panel configuration file is parsed and its items are loaded. The order in which these configuration files are parsed is the order of the comma-separated list of files defined in your tool_config_file setting in your config/galaxy.yml configuration file. The migrated_tools_conf.xml file is always parsed and loaded last.

If you uninstall a repository that contains tools, entries for those tools will automatically be removed from the shed-related tool panel config file and the integrated_tool_panel.xml file.

The best approach for managing the integrated_tool_panel.xml file is to allow Galaxy to add or remove entries as manually adding or removing them will likely result in undesired behavior. The order of sections and labels can be changed using a tool_conf_labels.xml file as described above.

My suggestion would be to backup what you have now (rename the existing integrated_tool_panel.xml to be something different - add the date or similar) then restart again to allow the file to be regenerated. If that is enough, then you can adjust using the methods above.

More examples for batching tool installs and managing these processes are covered in this tutorial. The UseGalaxy servers all do this. Occasionally there is some manual customization but the automation definately smooths it out.

Please give that a try and let us know how it works out! We can certainly follow up more. If I misunderstood and by “reloading” you meant that you already did this, would you like to post back the section of the file that is referencing the Qiime2 package? Then let us know which exact tool package you installed from the Main ToolShed? We can help to compare. :slight_smile: