I have a question about using a custom genome index with STAR in Galaxy.
I’ve created a genome index using STAR’s --genomeGenerate command on my local machine. In command-line STAR, I would typically use this index with the --genomeDir option during alignment. However, I don’t see this option in Galaxy’s STAR tool. Is this correct?
If there’s no direct way to use a pre-built index, does this mean that for using a custom reference genome in Galaxy’s STAR, we always need to provide the genome FASTA file and GTF file, rebuilding the index for each run?
Yes, the custom genome function is what is used at the public Galaxy servers, and it does recreate the index at runtime (and every time!). And while that also works on a local Galaxy server, it can waste a lot of resources.
Instead, you can do these two things. Both are done by the server administrator, and the results are available to users of that server.
Add in all of the indexes you see at public Galaxy servers to your local Galaxy server by mounting the CVMFS resource.
Then, layer in all of your own genomes as indexes using Data Managers. A Data Manager is a tool specific to administrators that runs all of the command line process to generate an index for a tool plus it populates the appropriate data tables in Galaxy – all as a special type of Galaxy job. You can run these individually in your browser, or better, in batches using special scripts.
