Hi @vebaev
Try this Data Manager as the first step when installing any new genome. If the database “dbkey” already exists, use that, or you’ll have problems (create duplicated indexes, which usually means starting completely over).
After fetching run a few other DMs that create basic indexes that Galaxy needs, then run DMs for specific tools. This post explains: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting
Thanks!