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.
> 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). -->
> <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> <plugin id="drmaa" type="runner"
> <handler id="main"/>
> <destinations default="local">
> <destination id="local" runner="local"/>
> <destination id="cluster" runner="drmaa">
> <param id="nativeSpecification">-t 12:00 -A noaccount/</param>
> <!-- 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"/>
> 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. -->
If I set up my test tool to run with this destination, it works.
>> On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
>>> I have some tools that run really quickly without using any kind of
>>> 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
>>> 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?
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>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: