On Tue, May 7, 2013 at 10:16 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
> On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker <dannon.ba...@gmail.com> wrote:
>> Hey Dan,
>>
>> Sure, you can configure per-tool job runners.  This wiki page
>> (http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started,
>> but let me know if you run into any trouble.
>>
>
> Thanks!
>
> Following up on this.
>
> As I mentioned before, this Galaxy instance was already configured to
> use the cluster by default. I did not set up the cluster or the Galaxy
> instance. This particular instance did not use the job_conf.xml file.
> But I updated it and set up a job_conf.xml and I was able to set it up
> so that some tools would be run on the local machine.
>
> However, in trying to get it set up so some jobs would run on the
> cluster (which is what happened by default before I came along) I ran
> into problems. Previously, it looked like the cluster stuff was
> configured in universe_wsgi.ini, and I guessed that these were the
> relevant lines:
>
> start_job_runners = drmaa
> default_cluster_job_runner = drmaa://-t 12:00 -A noaccount/
>
> So I tried to move that setup to job_conf.xml:
>
> ?xml version="1.0"?>
> <!-- A sample job config that explicitly configures job running the
> way it is configured by default (if there is no explicit config). -->
> <job_conf>
>     <plugins>
>         <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>         <plugin id="drmaa" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
>     </plugins>
>     <handlers>
>         <handler id="main"/>
>     </handlers>
>     <destinations default="local">
>         <destination id="local" runner="local"/>
>         <destination id="cluster" runner="drmaa">
>             <param id="nativeSpecification">-t 12:00 -A noaccount/</param>
>         </destination>
>     </destinations>
>     <tools>
>     <!-- Tools can be configured to use specific destinations or handlers,
>          identified by either the "id" or "tags" attribute.  If assigned to
>          a tag, a handler or destination that matches that tag will be
>          chosen at random.
>      -->
>         <tool id="mytesttool" destination="cluster"/>
>     </tools>
> </job_conf>
>
> When I run 'my test tool', however, it just hangs.
>
> Any tips?

To answer my own question...I think I have gotten this working, by
using the drmaa snippet from the job_conf.xml.sample_advanced file in
my galaxy distro:

        <destination id="real_user_cluster" runner="drmaa">
            <!-- TODO: The real user options should maybe not be
considered runner params. -->
            <param
id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
            <param
id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
            <param
id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
        </destination>

If I set up my test tool to run with this destination, it works.

Thanks,
Dan


> Thanks,
> Dan
>
>
>
>>
>> On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
>>>
>>> Hi,
>>>
>>> I have some tools that run really quickly without using any kind of
>>> cluster.
>>> I would prefer not to run these tools on a cluster, as the overhead of
>>> submitting these jobs makes them take much longer than they otherwise
>>> would.
>>> I have other tools that are computationally intensive and need to be
>>> run on a cluster.
>>> I would like to expose all these tools in the same Galaxy instance,
>>> but have some tools run on the cluster and others not.
>>>
>>> Is this possible?
>>>
>>> Thanks,
>>> Dan
>>> ___________________________________________________________
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>>
>>
>>
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