I am looking how to improve the import of BAM files into galaxy.
I often use the Upload tool in the Data Libraries to upload a number of BAM files into galaxy (after recombining several readgroups into a BAM file for the library, which I unfortunately have to do OUTSIDE of galaxy since it cannot take an arbitrary set of BAM files in a workflow)...

The UPLOAD tool seems to be correctly submitted to the cluster as you would expect, but then it seems that SAMTOOLS is run on each of the BAM files to create a index file (even though the directory already has one) on the server that is running galaxy, i.e. locally!

Is there a way to move the SAMTOOLS index creation into the upload tool so that it can be run in parallel on the cluster?


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