I am currently working on a few tools in galaxy which require both a bam and bam index. When I upload a bam to galaxy it, it correctly downloads the bam file and creates the bai metadata. In other words, I am noticing files being created in the following directories, under the galaxy naming convention, which are exactly the same size as the index and bam:
Now, I was under the impression that Galaxy handled bam and bai linking when a particular tool requires the bai (i.e. regardless, it makes the bai, so the tool will always have access to the bai whether or not it needs it). If this is not the case and I must somehow link the metadata to the bai can someone please let me know how to do that? I'm assuming a symbolic link would work, but I was under the impression that Galaxy took care of this.
Here is the Error I get from My Tool:
Missing bam index file: Path/To/Galaxy/database/files/000/dataset_3.dat
The current xml file is available here:
Thanks in advanced!