How to create BAM indices on cluster upon upload

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How to create BAM indices on cluster upon upload

thondeboer
Hi,

I am uploading a lot of data to our galaxy system, and it seems that the index creation is always happening on the server instance of the galaxy server and NOT on the cluster.

This seems to be particularly true for BAM files, where the index creation is being done on the galaxy server and it is done SERIALLY at that....This means that uploading 100s of BAM files can sometimes take hour upon hours...

I have a cluster with 500 cores so I was wondering how I can get GALAXY to create these indices on the cluster in a parallel fashion, in order to speed up the process....

It seems that the UPLOAD process IS kicked off on the server, but then the index creation for BAM files is done afterwards on the galaxy server itself...

Any help would be welcome...

Thon

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