adding reference genome to a local install

i am using a local install of galaxy and looking to add a reference genome. i used the “create dbkey and reference” data manager, and imported h38 genome. the fasta file exists on the server, but I can not see it listed as a reference genome in histat2 or any other tool. it does show up as a data table-- any idea what i need to do to make it show up as a reference genome?

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Some tools, such as hisat2, need an index built against that genome which is referenced in the tool’s tool_data_table_conf.xml.sample file. Looking at that file for hisat2, you’ll notice that it uses a table named hisat2_indexes. A data manager for that data table can be viewed at and installed from

There is also the option of using the galaxy reference data rsync server, detailed in this document.


Dave, thank you this answer is perfect. it helped debug how to trace these links through configurations. in addition to histat2, I fixed 3 other tool genome references by searching for the tool data table reference and adding the genome to the listing. thanks!

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Awesome, glad I could help. Feel free to get in touch if you come up with any other questions, I’m happy to advise.