Hello,
Has anyone recently succeeded in setting up a metagenomics analysis environment with Galaxy + QIIME 2?
I tried on both a Mac mini M4 (Apple silicon) and a custom-built PC running Ubuntu 22.04.
I can install QC-related tools (e.g., FastQC, MultiQC) successfully, and QIIME 2 itself appears to install correctly from the Tool Shed.
However, the QIIME 2 tools do not show up in the left-hand tool panel inside Galaxy, even though they appear under “Installed Tools” in the Admin page.
I have tried many things, but it still doesn’t work — I suspect this might be a bug or an indexing problem.
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.
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.
Reinstalled QIIME 2 via Tool Shed (and via shed-tools / ephemeris)
→ The new integrated_tool_panel.xml was generated successfully, but still does not contain any QIIME 2 tool entries. shed_tool_conf.xmldoes list the QIIME 2 repositories (for example, qiime2_import, qiime2_feature_classifier), and they appear under Admin → Installed Tools in the UI.
Here are some short excerpts:
From integrated_tool_panel.xml (no qiime2 section):
Do you have any ideas why the QIIME 2 tools would appear in Installed Tools and shed_tool_conf.xml, but still fail to appear in the tool panel? Could this be related to the toolbox_filter / YAML panel system introduced in newer Galaxy versions?
If helpful, I can share:
full integrated_tool_panel.xml
the galaxy.yml entries for tool_config_file, shed_tool_conf.xml, and tool_data_table_config_path
startup log excerpts around metadata updates.
Thank you again for your help!
Thanks for explaining and testing! There might be a known issue (not confirmed yet). Since there aren’t any comments yet, and this user was installing custom tools (not from the ToolShed), I wasn’t originally sure if this is your use case or not.
The Docker build completed successfully without any errors. According to the build log, the tool installation also proceeded without any issues. However, when I run the Galaxy instance, the installed tools are not visible, and the galaxy/database/shed_tools directory is missing—despite the shed-tools install command completing without errors.
Can you replicate this? A missing galaxy/database/shed_tools directory?
sudo docker exec -it galaxy2005_qiime2 bash
ls -l /galaxy-central/database/shed_tools
ls -l /export/galaxy-central/database/shed_tools
Output:
Error response from daemon: container <id> is not running
ls: cannot access '/galaxy-central/database/shed_tools': No such file or directory
ls: cannot access '/export/galaxy-central/database/shed_tools': No such file or directory
So yes — the container was stopped, and both shed_tools directories do not exist.
This exactly matches the behavior described in GitHub Issue #622 (“Extending the Docker Image (Galaxy 24.01, 24.02) does not work”).
I’ll comment on that ticket as well to confirm this replication from my side (Mac mini M4 / Ubuntu custom PC).
Thanks again for catching this so quickly!
Haha, not so quickly but it clicked today! And yes, knowing that this is happening for even ToolShed tools is a big deal. They will definitely appreciate the feedback.
Environment
What I have already tried