Reference data: no option available
Contact the administrator of this Galaxy instance if you miss reference data (–config-dir)
For immediate use, try using the custom genome feature.
If you need to assign a database metadata to datasets, your custom genome can be promoted to a custom build.
For use later on, please post back details about the genome and we can consider adding it to the native reference indexes. We’ll need enough information to locate the data, and the genome should be from a public source. Not all genomes can be added but it doesn’t hurt to ask 
I had previously created a custom genome for my species (with a mitochondrial genome) and followed both steps. However, these custom genomes are not enabled in the “Reference data” field of Get Organelle from reads.
However, Get Organelle does not expect a reference genome as a mandatory parameter, but rather a database from a clade. Can you please validate this for me?
Ok, thanks for explaining. Please try the tool at UseGalaxy.eu since they have more indexed data specific for this tool.
To be clear to anyone reading: Custom genome functions work with the vast majority of tools – and are for when a single genome is needed. This guide explains how it works → Reference genomes at public Galaxy servers: GRCh38/hg38 example ← along with a bit of extra help for human variants, but the same process works for any fasta file that you want to use as a reference (genome, transcriptome, exome – all)
The few tools that do not compare to a single genome, but a merged index of several genomes or parts of genomes (organelles), are a different comparison analysis concept and do sometimes require a special server-side index. At least one of the public UseGalaxy servers likely hosts what you need – so please check first, then ask and we’ll try to address anything still needed. Be specific: server URL, tool name/version, and the exact reference index you cannot find and cannot use the custom genome functions to resolve.
A post was split to a new topic: Custom reference genome troubleshooting