Kraken2 reference index mixup

One of the Kraken2 indexes is an exact duplicate of another, instead of containing the actual distinct data.

So -- this needs a new index to be created (or found?), and replaced over the existing incorrect file. From what I can tell, impacts all usegalaxy servers and any others using the CVMFS mount.

If I can help with this, I will, but I'm not sure where the originals are being created. I should already have access to CVMFS and probably can figure out the transfer details etc.

Compare, these are nearly the same. Missing plants?

http://datacache.galaxyproject.org/managed/kraken2_databases/2022-09-05T092205Z_standard_prebuilt_pluspfp_2022-06-07/inspect.txt
http://datacache.galaxyproject.org/managed/kraken2_databases/2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07/inspect.txt
Ran some comparisons in this history. Differences are minor, and look more like database updates rather than an entirely new kingdom added/missing. https://usegalaxy.org/u/jen-galaxyproject/h/kraken2-indexes

Seems to have been introduced upstream, not just in CVMFS, since presents at EU as well. Ticket at EU:

Reported at https://help.galaxyproject.org/t/kraken2-databases-mixed-up/11290/6

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Reported at
* https://help.galaxyproject.org/t/kraken2-databases-mixed-up/11290

Consolidated from
* https://github.com/galaxyproject/usegalaxy-tools/issues/672
* https://github.com/usegalaxy-eu/infrastructure-playbook/issues/1071

Start by comparing the two linked inspect.txt files and the Kraken2 index history in the linked Galaxy history. Review the linked help.galaxy.org report and consolidated issues to identify the intended source of the distinct index and how it is distributed through CVMFS. Done means the incorrect index is replaced with verified data across the affected servers.

Written by the indexing model from the issue text.