various-job-conf-galaxy

job_conf-galaxy

job.conf.xml file	description	issues
chronos_job_conf.xml	configuration to run galaxy in a apache MESOS cluster	the jobs are run but there are problem in linking the results in the history, the runner chronos.py called by the chronos destination block have some lack: is not possible to attach other volumes (as cvmfs for refdata) and the job is not executed in the default working directory and this parameter can not be set
docker_default_local_job_conf.xml	configuration to run galaxy with jobs dockerized by mulled	the configuration work without problems is also possible to attach cvmfs volumes for refdata some of the tools can't be run with mulled, for this reason is better to specify the tools that run with Conda in the tool block
singularity_job_conf.xml	configuration file to run jobs in Singularity container	it works well with attached cvmfs volumes (one for singularity images, /cvmfs/singularity.galaxyproject.org, and one for refdata) but the version of galaxy must be >= 18.09 because only in this version the development team add the singularity block xml <param id="singularity_image_dir">PATH</param>
docker_optional_job_conf.xml	configuration to run specific tools that supports Docker container in a different destination	using dynamic runner and docker_dispatch destination xml <destination id="docker\_dispatch" runner="dynamic"> tools that supports Docker container are directed to a different destination (local_docker), in this configuration the docker container are run with sudo