I have been using Galaxy for a few months now, and lately I had to redo an old Trinity assembly and came back to the server. After setting everything i executed and the proccess has been queued up for more than one day now, I have tried setting new instances and always happens the same. Other programs seem to be working fine. Have trinity jobs been paused for now? Is there a fix for this problem?
Some tools will queue longer than others, and how long any tool queues varies daily.
Clusters than executed assembly tools, including
Trinity are usually busy. Why? The tools are computationally expensive so jobs run longer and the cluster nodes turn over for new jobs slower.
The best advice is to queue jobs up and let them run. Avoid deleting and rerunning, as that places the new jobs back at the end of the queue, extending wait time. If done often enough, jobs may take a very long time with all the restarts!
If you didn’t know: you can set a notification on tool forms to email yourself once jobs are done Also, consider using collections and workflows. Workflows queue up tools/jobs in batch (and also has an email notification feature) and collections group similar dataset together. If you are not sure how to use those, search with the keywords here: https://training.galaxyproject.org/