Hi Simon, This should work, it looks like there may be a bug with handling tool shed IDs when determining job destinations. You are actually supposed to be able to use any of:
shed_host/repos/owner/repo/tool_id/version shed_host/repos/owner/repo/tool_id tool_id I'll take a look at this as soon as possible. One thing you might try in the short term is using the percent encoded tool id in the <tool> tag in job_conf.xml: toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0 --nate On Sep 10, 2013, at 10:35 PM, Guest, Simon wrote: > 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 > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. 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