On Tue, Apr 22, 2014 at 1:59 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> 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.

You are right of course - very sorry. Dynamic destinations and macros
would make sense if there was some way to alter the environment based
on the destination - which I am not sure is possible with
nativeSpecification at least generally. (It sounds like you can with
PBS/Torque).

Here is patch that would add the ability to specify <env
id="NAME">VALUE</env> tags to job destinations in job_conf.xml and
have them auto-populated in jobs.

https://github.com/jmchilton/galaxy-central/compare/job_env?expand=1
https://github.com/jmchilton/galaxy-central/commit/d05e15d712c9a3175552e7c5f7041301507dae1f.patch

Any interest in testing it for me :)?

If not, I can open a PR for it as it is.

>
>
> 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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