No worries, we’re here to help as much as we can!
If you transfer files using Galaxy, they’re best used in Galaxy. Its not really a simple process to access them using the command line later.
The best way to transfer files to work on using the command line is to use an SCP/FTP client. If you’re using Windows, then WinSCP is popular, or FileZilla on MacOS/Windows.
Generally, these software packages present your local filesystem on one side of the screen, and the remote filesystem on the other. You can then drag-and-drop files from your PC/laptop onto your VM. Generally, the process is pretty self-explanatory, and there are lots of good beginner’s guides for each software package.
The only stumbling block is to remember that your instance IP address (which you can see at https://bryn.climb.ac.uk) is the “Hostname” of the remote server that you’re connecting to, and the username (if you’re using GVL) is