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

Technical Support
1

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.

:magnifying_glass_tilted_left: Environment

  • Galaxy container: bgruening/galaxy-stable:latest (2025-10 build)

  • Systems tested: Mac mini M4 (Sonoma) and Ubuntu 22.04 (Intel i5-8400)

  • Network: proxy-free local environment

  • Admin rights: enabled (set admin_users: in galaxy.yml)

:brain: What I have already tried

  • Rebuilding the tool search index and resetting metadata

  • Re-starting Galaxy and re-loading integrated_tool_panel.xml

  • Checking paths in tool_config_file and tool_data_table_config_path in galaxy.yml

  • Installing QIIME 2 from both the main Tool Shed and test Tool Shed

  • Verifying ownership/permissions in /export and /galaxy-central/tools

  • Re-installing via shed-tools install (ephemeris 0.10.10)

Despite all this, QIIME 2 never appears in the left panel.
Has anyone experienced the same? If so, how did you fix it?

Thanks in advance for any advice.

こんにちは。
最近、Galaxy + QIIME 2 でメタゲノム解析環境を構築できた方はいらっしゃいますか？

Mac mini M4（Appleシリコン）と Ubuntu 22.04 自作PC の両方で試しました。
Galaxy 内で FastQC や MultiQC などの QC 系ツールはインストール・動作しますが、QIIME 2 自体は導入できても、左側のツールパネルに表示されません。
管理者画面（Admin→Installed Tools）には QIIME 2 が見えています。

いろいろ試しましたが解決できず、ツールパネルのインデックスや Galaxy 側のバグの可能性を感じています。

環境

  • Galaxy コンテナ: bgruening/galaxy-stable:latest（2025年10月版）

  • 使用OS: Mac mini M4（Sonoma）／Ubuntu 22.04（Intel i5-8400）

  • ネットワーク: プロキシ無しのローカル環境

  • 管理者権限: galaxy.yml で設定済み（admin_users）

試したこと

  • 「Reset metadata」「Rebuild tool search index」などを実行

  • integrated_tool_panel.xml の再読み込み

  • galaxy.yml の tool_config_file / tool_data_table_config_path を確認

  • Tool Shed（main / test 両方）から再インストール

  • /export や /galaxy-central/tools の権限確認

  • shed-tools install（ephemeris 0.10.10使用）による再導入

これらをすべて試しても、ツールパネルには QIIME 2 が出てきません。
同じ症状を経験された方がいましたら、解決法を教えてください。

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3

Hello @HKadokawa,

I am not sure why your tools are not showing up, but I can tell you the tools we distribute for usage with Galaxy are from our Amplicon distribution which is not for meta genomic analysis. If you want to do meta genomic analysis, you will want to use Moshpit which can be installed via the instructions here and used via the command line.

If you would like to use QIIME 2 Amplicon through Galaxy, we actually distribute our own ready made Docker containers for that on Quay. In addition, usegalaxy.eu and cancer.usegalaxy.org host QIIME 2 tools, but cancer.usegalaxy.org's are very outdated.

I would strongly recommend against trying to create a Moshpit Galaxy container. It may well not even be fully possible, and if it is the process will be quite involved. We don't bother doing it ourselves because Moshpit requires a very large amount of resources which are better managed via the command line.

Thank you,
Anthony Simard

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