On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> I'm wondering if it is sensible to make Galaxy tools automatically use
> the environment variable $NSLOTS to automatically adjust their
> number of threads?
> Using $NSLOTS works on SGE, but is it generally used on other clusters?
> The idea here is rather than hard coding the number of threads in a tool
> or its XML file, which may need to be altered for different local setups, and
> it can be specified in universe_wsgi.ini under [galaxy:tool_runners]

Actually thinking about this over lunch, you wouldn't want to evaluate
the $NSLOTS variable when the XML <command> is processed, as
that would be done on the server not the cluster node. In some cases
then embedding $NSLOTS in the command string (suitably escaped)
should work, otherwise doing it in a wrapper script seems best.

> Would this work in principle on other cluster setups? i.e. Is $NSLOTS
> sufficiently general?

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