Thanks again Nate.

You are right that SGE is overwriting TMPDIR.
When the job runs, TMPDIR is actually set to a job specific dir like

It seems that I will have to change the SGE queue settings so that TMPDIR
only set the "prefix" to /scratch that I want... but this would affect all
users of the queue...

We will probably have to live with that.
Thanks for all your help!

You might want to have a dummy tool output `set` on the cluster.  Chances
> are that SGE is overriding $TEMP or $TMPDIR at job runtime.  You may need
> to set this in ~/.sge_request or use Galaxy's environment_setup_file option.
> --nate
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