I am having trouble getting a toolshed tool to be dispatched to the destination I list in the job_conf.xml file.

 

My job_conf.xml file looks like this:

 

<?xml version="1.0"?>

<job_conf>

    <plugins>

        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="20"/>

        <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />

    </plugins>

    <handlers>

        <handler id="main"/>

    </handlers>

    <destinations default="condor">

        <destination id="local" runner="local"/>

        <destination id="condor" runner="condor">

            <!-- With no params, jobs are submitted to the 'vanilla' universe with:

                    notification = NEVER

                    getenv = true

                 Additional/override query ClassAd params can be specified with

                 <param> tags, e.g

            <param id="request_cpus">8</param>

            -->

        </destination>

    </destinations>

    <tools>

        <tool id="upload1"                              destination="local"/> <!-- Upload File -->

        <tool id="ucsc_table_direct1"                   destination="local"/> <!-- UCSC Main -->

 

        ... stuff omitted ...

 

        <tool id="toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS: infoseq46/5.0.0"        destination="local"/>

    </tools>

</job_conf>

 

 

So, you can see I have a default destination of condor, but I'm trying to run my toolshed EMBOSS infoseq tool on local.  However, it is stubbornly running on condor.

 

In lib/galaxy/tools/__init__.py:1132, I see this comment which got me wondering:

        # In the toolshed context, there is no job config.

 

Is it possible to define tool destinations for toolshed tools?  Are there some gotchas that I should know about?  Any other ideas why my job is ignoring the config in job_conf.xml?  (By the way, I can change say the upload1 tool to run on Condor by setting its destination in that file, so it is doing something.)  The other thing I saw in the source code is stuff about old_id and toolshed guids.  Do I need to understand this stuff?

 

The paster.log contains the following when I submit the infoseq job:

 

147.158.130.216 - - [11/Sep/2013:13:53:34 +1300] "GET /tool_runner?tool_id=toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0 HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/" "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0"

147.158.130.216 - - [11/Sep/2013:13:53:40 +1300] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/tool_runner?tool_id=toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0" "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0"

galaxy.jobs DEBUG 2013-09-11 13:53:40,886 (92) Working directory for job is: /home/galaxy-dev/galaxy/database/job_working_directory/000/92

galaxy.tools DEBUG 2013-09-11 13:53:40,886 Tool::get_job_destination: {'runner': 'condor', 'legacy': False, 'params': {}, 'tags': None, 'url': None, 'converted': False, 'id': 'condor'}.

galaxy.jobs.handler DEBUG 2013-09-11 13:53:40,894 (92) Dispatching to condor runner

 

(I added the debug output for Tool::get_job_destination to see what was going on.)

 

Any ideas?

 

cheers,

Simon