Welcome, @readlikeabook
Yes, posting questions here is how to get the fastest feedback.
I reviewed your jobs earlier today and wrote back.
Two important parts:
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The first condition must be labeled as Condition (exactly and only – it is just how Bioconductor wrote the tool as far as I know!)
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Put all of the peaks and BAM datasets into collections, and make sure these are in the same sort order so that the tool can “match up” a peak file with a BAM file.
This will mean a minimum of four collections for two conditions. You can create these using two collections of fasta files (then map, filter, call peaks) to start with or you can organize your uploaded data after. Keep the element identifiers very simple (or, adjust to be simple) or the tool will have a different sort of trouble.
Your input collections should look something like this. Notice how simple the names of the collection are. If the element identifiers were exacted, those labels are also very simple and in the same order between peak-bam sets. By “simple” I mean these are R friendly: Letters, numbers, no spaces, not starting with a number, optional underscores (the only special character allowed).
If you are not sure how to manipulate data inside collection folders, this tutorial is a sort of “cheat sheet” → Hands-on: Using dataset collections / Using dataset collections / Using Galaxy and Managing your Data
And more tips for Bioconductor tools are in here. → FAQ: Extended Help for Differential Expression Analysis Tools
If you get stuck, you can share back a link to your history and we can use it as an example while I help you to get it organized in a way this tool can understand. 
ps: The error message about “memory” can mean a job is actually too large to process at the public clusters, but that is somewhat rare. It is much more likely that a tool ran away due to problems with the inputs – content or labeling – so that is what we are exploring first. More about that catch-all error → FAQ: Understanding 'exceeds memory allocation' error messages