Hi John,

Am 22.04.2014 20:45, schrieb John Chilton:
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 problem with multiple variants (multiple handlers) is that I only can specify one ENV variable that is known to the current shell. I don't think I can set the variable directly inside the nativeSpecification tag, or? Moreover, the variable need to have the name _JAVA_OPTIONS. To solve that I need to set the variable somehow inside the nativeSpecification tag.

Dynamic destinations may work, but what happens if I change a ENV inside of python ... it is not known to the parent process or? Even if it is known, is it only known to that specific tool?

The memory card referenced above might help, but a much easier cards
might help this would be...

https://trello.com/c/t1FH1Q5P


Yes, but that is really hackish :). If there is no other way, I will try something like that ...

Also tool style macros for job_conf.xml might help right - keep size
of XML down?

https://trello.com/c/wt1LflNh

Unfortunately, macros do not work here. In GATK different tools do have different requirements. I can probationally work around that with HEAP_SIZE/2 or something like that, but a job_conf.xml based solution would be better.

Feel free to create another card for this request (allowing
parameterized tools to influence destination parameters) - seems
reasonable.

Ok I will wait a few more hours and than create such a card.
Thanks for your ideas,
Bjoern




-John

On Tue, Apr 22, 2014 at 1:32 PM, Björn Grüning
<bjoern.gruen...@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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