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?
1 Like
Hello,
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 https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_hisat2_index_builder/
There is also the option of using the galaxy reference data rsync server, detailed in this document.
3 Likes
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!
1 Like
Awesome, glad I could help. Feel free to get in touch if you come up with any other questions, I’m happy to advise.