Genome index or dbkey not accessed by tools on a local Galaxy - Solution: Run tool-specific Data Managers

[jennaj]

Hello @pa.saunders!

You’ll need to run more Data Managers. This prior Q&A lists the best order to run these for base-line setup. After those four are done, then use the HISAT2 DM to create indexes for that tool, and run any other DMs for indexes used by the other tools you plan to use.

Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Hi, The mm10 reference genome/build is sourced from UCSC. You’ll need to index the genome on your server with Data Manager tools. Install the genome with Data Managers (sourced from the ToolShed, all are in a separate category there). Install DMs like any other tool using the Admin functions. You’ll need these DMs at a minimum. Execute them in this order first: Fasta fetcher – has an option to pick UCSC as the data source. SAM indexer Picard indexer 2bit (twoBit) indexer Then get the DMs…

Thanks!