Even if you already have the human genome, you might want to let the Data manager fetch the genome from the source (if it is a source listed on the DM). Or you can put your fasta version into the same history that you run DMs from, and input the fasta on the DM form as the "source from the history".
Rerunning the DM for BWA would be an easier way of getting the index into Galaxy (instead of manually adding in an existing index). But this is your decision.
Both choices are explained here, plus there is a DM tutorial: https://galaxyproject.org/admin/#data-resources
Thanks! Jen, Galaxy team
Hi, Thanks for your answer. I did as you mentioned and there is both reference genome (.fa) and index in data library. However, when I want to use FreeBayes tool, there is no option to use my local reference genome. How can I fix it?