Hi,

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" destination="10G_memory">
<param id="nativeParam">export _JAVA_OPTIONS='-Xmx=6GB'</param>
</tool>

Thanks!
Bjoern



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