Hello, I am new-ish to Galaxy. I’m trying to run a smaller job - just Join two Datasets on a normalized count file with a list of significant genes file - and it’s stuck in Waiting to run. I tried re running the job several times, but it’s still stuck. I gave up on it and started some other jobs for a different analysis in the same history, and those are starting and finishing fine. Generally I would just wait, but it seems odd to be stuck on a smaller job but be able to do larger jobs. Is there something wrong with the job I’m trying to do? I’m just at this tutorial step https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#hands-on-extract-the-normalized-counts-of-the-most-differentially-expressed-genes using my own data.
Welcome, @ebrandt
Different types of tools get routed to different clusters, and which cluster happens to be free for new jobs changes all the time. So, what is going on seems normal.
And remember, every time you delete and rerun a job, that new jobs is added back to the end of the queue again. If you do this often enough, a job may never get the chance to move up and actually run. So, try to leave queued jobs queued.
Later on, you can use a workflow. Or, you could use one now since each tutorial includes a workflow template. 
Using a workflow queues all of your jobs at once!
More details
Hope this helps!