Sorry for the delay, the Galaxy EU https://usegalaxy.eu has been undergoing many changes.
Kraken tool already has indexes added at Galaxy Main https://usegalaxy.org, so using the tool there is an alternative for now. Galaxy AU https://usegalaxy.org.au/ is also a choice. Both include Bacteria.
Kraken tool could have indexes added at Galaxy EU. The administrators would need to make that decision. Ping @hxr @bjoern.gruening @wm75
Kraken2 tool suite is currently having the associated Data Manager updated (a tool that installs the indexes). It is not quite ready to be used yet, and probably is why you don’t see those indexes at the EU server now.
Kraken2 is not installed at Main or AU yet (primary tools or DM), but I expect that we will add it/create indexes at Main once the DM is ready for use. Not sure about AU, @Slugger70 can comment more if he wants, but I would expect about the same answer.
Please feel free to ask for an update in about a month if you don’t see the indexes/tool versions updated at these public servers.