I have installed a local fresh Galaxy instance. Last time I remember I had some Data manager allowing me when I’m in the tool to select from all “remotely” reference genomes and it was instantly fetched and indexed. Unfortunately, I do not remember how I accomplished that and now my ref genome drop-down menu is empty. It was looking like:
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
The strange thing is that in the old instance there were no installed genomes, and in for example Bowtie the drop-down menu for reference genome it was showing all available (like hundreds of them) and then I start Bowtie and select ref genome, then it was remotely downloaded and mapped to it…
Your picture also shows a list of genomes on the Bowtie data manager.
It is certainly possible to create just the Bowtie index, and that will create some associated data indexes, but expect to have problems later on if you also do not index for samtools, etc.
Indexing genomes that way I listed avoids many many problems. Odd tool errors, metadata problems, …