As your Galaxy instance becomes more production ready I would
definitely recommend installing a job queue such as grid engine,
Torque, or SLURM. For this simple use case though, you should be able
t define multiple local job runner instances to ensure only one
Trinity job runs a time.

Your job_conf.xml should look something like this:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <plugin id="local2" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="local">
      <destination id="local" runner="local"/>
      <destination id="local2" runner="local2" />
    </destinations>
    <tools>
      <tool id="trinity" destination="local2"/>
    </tools>
</job_conf>

Hope this helps.

-John

On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya <ccanch...@gmail.com> wrote:
> Hi adam,
>
> So far we have just a standalone server since we are still setting up our
> tools (we will scale up to our sge cluster, though). Any clue how to limit
> jobs per tool basis?
>
> Best,
>
> Carlos
>
> On Saturday, September 21, 2013, Adam Brenner wrote:
>>
>> Carlos,
>>
>> Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being
>> dispatched to your node(s)? More info here:
>> http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
>>
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> aebre...@uci.edu
>>
>>
>> On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya <ccanch...@gmail.com>
>> wrote:
>>>
>>> Hi guys,
>>>
>>> I have a running local galaxy installation on one of our servers.  I've
>>> just installed Trinity for de novo assembly of transcripts and it will use
>>> up to 32 processors. However i would like to limit the number of concurrent
>>> jobs only for this tool. Do you know if it would be possible to limit the
>>> number of concurrent jobs per tool basis?
>>>
>>> Bests,
>>>
>>> Carlos
>>>
>>> --
>>> Carlos  Canchaya
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>>
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>>
>>
>
>
> --
> Carlos A. Canchaya
> Universidade de Vigo
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
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