You can create multiple variants of the 10G_memory tool with different
native specifications right? Does this work around result in too much
XML? Dynamic destinations could also be used - if you are interested I
could post a demo rule that you might be able to use.
The memory card referenced above might help, but a much easier cards
might help this would be...
Also tool style macros for job_conf.xml might help right - keep size
of XML down?
Feel free to create another card for this request (allowing
parameterized tools to influence destination parameters) - seems
On Tue, Apr 22, 2014 at 1:32 PM, Björn Grüning
> to specify -Xmx and -Xms for java based programs I set my preferred values
> to $_JAVA_OPTIONS and include _JAVA_OPTIONS as nativeSpecification with -v
> _JAVA_OPTIONS. That worked good so far, but the downside is that I can not
> have different options for different tools. Is there a trick I can specify
> arbitrary $ENVs to a specific tool? Any ideas how to solve that, without
> hacking the -Xmx and -Xms parameters into the wrapper file?
> It is related to https://trello.com/c/HGEYPQf6.
> I would be interested in workarounds until that card is closed :)
> Something like that would be great:
> <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner"
> <param id="nativeParam">export _JAVA_OPTIONS='-Xmx=6GB'</param>
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