Troubleshooting

The Galaxy UI provides most of what you might need to troubleshoot users failed analysis.

A useful tool is the ability to impersonate a user and view their data without having to log in using their credentials. To do this, log in as an admin. Go to the Users panel in the Admin section. Find a user you want to impersonate and click the [v] arrow beside their email address. Select impersonate. This will reload the Galaxy UI and you will now be able to inspect the users histories and data from their point of view.

To find an errored dataset in a history, type state:error into the search box above. Remember to click the "Show hidden" button to view all datasets. You can try clicking on the "Run job again" button on the dataset tile and re-execute the job to see if it is a transient issue. If you click the "i" dataset details button on the dataset tile, Galaxy will provide detailed information about the jobs execution. This is usually the best place to look for errors.

If the issue was not with a specific dataset, then another useful place is to look at the logs of both the galaxy-app and galaxy-worker containers. The logs location depends on how Galaxy is deployed, see your deployment destinations documentation on how to access container logs. galaxy-app will show errors related to API access and the front end business logic. galaxy-worker containers are responsible for the scheduling of workflows and jobs, look at their logs to see if there was an issue with scheduling.

A common issue you may find is the job will report "Command not found". This is usually due to Galaxy being unable to determine the biocontainers container required by the tool, so it defaults to the Galaxy container. Check the logs for Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [None] errors. This indicates that there was an issue connecting to https://quay.io/biocontainers to lookup the container, or a tool has been upgraded in Galaxy and its dependencies are not provided by a container. If the Galaxy tool wrapper has a single dependency, then the tool must be available from biocontainers. If the tool has multiple dependencies, check with the maintainers of BioContainers/multi-package-containers and planemo-monitor.