Hello Galaxy,

I'm currently working on adding some tools and am having an issue with DELLY.

So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy.

There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index.

I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how.

Any help is greatly appreciated,