On Tue, Jul 26, 2011 at 10:39 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Tue, Jul 26, 2011 at 5:16 PM, Duddy, John <jduddy@illumina.com> wrote:
> I can give you a very good example - if you are doing alignment and for some
> reason need to convert the input file before operating on them, such that you
> need a complete copy, /tmp may not have enough room. I have had this happen
> to me running lots of instances of an aligner, temporarily using 100G+ of temp space.
>
> I don't see the need to have a "shared" temp space, but I do see the need to
> be able to tell the tools where you want them to put temp files.

So in your setup, the cluster nodes are not likely to have 100G+ on /tmp (i.e.
the local hard drive of the node), so you want them to use a temp folder on the
cluster shared storage?

I think needs will differ between tools - in some cases you really want
a fast local drive for temp files, and putting them on a network drive
will just kill performance. Using /tmp seems a safe default.

Is there any guidance for tool authors on where to put temp files, and
how to access any related Galaxy settings? There is nothing currently
listed here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Peter
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