I recently installed a local instance of galaxy (v18.0) on a linux server and configured galaxy to work with apache and proftpd. The galaxy worked well when there is no job_conf.xml given under config/ directory. The galaxy could start without errors when job_conf.xml is used (job_conf.xml is just a copy of job_conf.xml.sample_basic) , but all jobs submitted stayed as gray and can't be pushed to "running" status. The galaxy documentation states that galaxy runs with the configuration as defined in job_conf.xml.sample_basic when no job_conf.xml is given in config/ directory, so I assumed that galaxy should work with or without job_conf.xml. Did I miss something?
In the old version of galaxy, we can define tool_runners in universe_wsgi.ini file. The jobs run in local can be defined such as "cat1 = local:///" and the jobs run in cluster can be defined such as "tophat = drmaa://-pe galaxy 4". Can I copy the tool_runners defined in universed_wsgi.ini to galaxy.yml file used in the new version of galaxy? If it is necessary to configure them in job_conf.xml, is there an example file I can use as reference (for example, cat1 run locally and tophat run in computing node/cluster)?
Thank a lot for your help!