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... https://trello.com/c/t1FH1Q5P Also tool style macros for job_conf.xml might help right - keep size of XML down? https://trello.com/c/wt1LflNh Feel free to create another card for this request (allowing parameterized tools to influence destination parameters) - seems reasonable. -John On Tue, Apr 22, 2014 at 1:32 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
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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