Hi @frans
So … maybe these were just examples, but… when using the CVMFS reference http://datacache.galaxyproject.org/
Both sacCer3 and Arabidopsis_thaliana_TAIR10 are already indexed in CVMFS, yes? If true, then if there is some tool specific index you want to create that is missing, you can use the already indexed genome (referenced by the database dbkey) to create a new tool-specific index.
You should see those databases as a local option in the BWA Data Manager. But, I also see BWA indexes for these two already.
And for the path changes, yes, you won’t be able to write to CVMFS. But you should be able to read from it. Your problem here also points to a CVMFS connection issue.
What am I misunderstanding about your question? Were you not able to get CVMFS installed on your server? Would you like to solve that first? Share more details about what was going on with that and we can try to help.
XRef
For completely new genomes and associated indexes, this topic has the general details. In short, get the genome indexed (fasta idx, samtools, picard), then generate tool specific indexes, as wanted, but after. Why? tool specific indexes tend to use the fasta/samtools/picard indexes to generate new indexes (anywhere, not just Galaxy). Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting - #2 by jennaj. You can do all that manually if you are careful enough (tedious, error prone, but possible, that’s what the “hands-on” in CVMFS is! all of our pre-data manager content), or in a batch stream with Ephemeris (exact, reproducible, and highly recommended if at all possible) Hands-on: Galaxy Tool Management with Ephemeris / Galaxy Tool Management with Ephemeris / Galaxy Server administration.