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