Importing .fastq files from a server into Galaxy running on the same server


I'm excited to implement Galaxy to run Qiime2!

We have our own server where we store data and where I have been (slowly and agonizingly) running Qiime2 via the command line (we are on version 2022.2). My collaborators over in the CS department have gotten Galaxy running on the server and I'm ready to use it with our data. However, at the moment, it seems that Galaxy cannot import .fastq files from the same server it's running on - instead, I'll have to download them to my laptop and them upload them back into Galaxy. The CS folks and I are hoping there is a better way to do this, since the files are large and there are a number of them.

Any tips/advice for going about this?

And, second question: my sequencing files are already split apart by barcode, and I have paired end reads. I've been using PairedEndFastqManifestPhred33V2 as the input-format for the import tool, but that option isn't in the drop-down menu - however I do see "MultiplexedPairedEndBarcodeInSequence" as an option, and, as my barcode is still in the sequence, I assume this is the option I should use. Let me know if there is a better one!

Thanks for your help on this.