On Thu, Feb 9, 2012 at 2:57 AM, Fields, Christopher J
<cjfie...@illinois.edu> wrote:
> Forgot to add, but this also seems tied to the same problem
> Ryan's describing.  IIRC Galaxy also runs 'samtools sort' after
> certain jobs, correct?
>
> chris

This sounds like part of the "BAM grooming" (assuming that's
what the Galaxy team call it, based on their term "FASTQ
grooming") which tries to ensure BAM files are coordinate
sorted and indexed on upload/import etc.

Perhaps this is a general symptom of file format conversion
also being done on the server rather than as a cluster job?

Peter

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