simple job_conf.yml example

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1

Hi all,
I have a local Galaxy instance running in Ubuntu on a workstation. Up until Galaxy v22.05 I used a very simple job_config.xml to control the number of workers and how many cores the job will run on. It looks like this:

<?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"/>
    </plugins>
    <destinations>
        <destination id="local" runner="local">
<param id="local_slots">16</param>
</destination>
    </destinations>
</job_conf>

First I wanted to upgrade the v22.05 to 23.1 but with the git pull command it said that the server is already up to date. I then installed a fresh v23.1 but realized that this version does not use the job_conf.xml anymore, has a sample job_conf.yml but no simple job_conf.yml.sample file. I was not able to change the job_conf.yml to get jobs run on more than one thread.

Could anyone please provide me with a simple job_conf.yml similar to the job_conf.xml posted above? Or help me how to run v23.1 on multiple threads on a local machine?

Any help is appreciated! Thanks a lot!

2

I believe the job_conf.xml is supported in 23.1. Maybe try verifying that Galaxy found it by checking the startup logs.

3

your yml version would be something like the following

runners:
  local:
    load: galaxy.jobs.runners.local:LocalJobRunner
    workers: 4
execution:
  default: local
  environments:
    local:
      runner: local
      local_slots: 4
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4

Thanks a lot for your fast answer!

And you are right, the job_conf.xml is still supported. As per your suggestion I checked the log and it turns out that the required location has changed: In v22.05 I placed the job_conf.xml in the ~Galaxy/config folder while v23.1 is looking for it in ~/galaxy/lib/galaxy/config/sample. Copying the job_conf.xml there solved the problem and my local installation is running on multiple cores now.

Thanks again!

1 Like