I am not sure exactly what you mean, but if what you want to be able to do is have your custom reference genome available to tools within a workflow (to select as a target "database"), then do the following:
- Clean-up the custom reference genome fasta file with the tool NormalizeFasta using the option to wrap at 80 bases and to trim the title line at the first whitespace.
- From within the history that contains that custom genome fasta file, go to User > Custom Builds.
- Create a short, one word (no spaces) name to the build.
- The same value can be used for the description.
- Select the cleaned-up custom genome.
- Submit. Allow this to process.
Your custom build will now appear in the list of cached genomes and can be used with tools (as a "database" assignment) and within workflows.
Thanks! Jen, Galaxy team