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Select which EFI to use while booting Macbook Pro

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I installed Ubuntu 16.04.1 LTS to a flash drive (I also told the installer to install the bootloader there) last night and discovered this morning that I could boot Ubuntu simply by inserting the flash drive with the computer turned off and then turning the computer on. No holding down option and selecting boot media; it just automatically booted Ubuntu. I then noticed that if I shut down the computer and removed the flash drive that the computer would boot into GRUB next time I turned it on (again, without selecting boot media). I though this was odd, since I had told the Ubuntu installer to put everything on my flash drive. I later decided that I wanted the computer to boot OS X (I have Sierra 10.12.2) automatically instead, so I booted OS X by holding option on boot and selecting Macintosh HD as boot media, then in system preferences I went to select startup disk and chose Macintosh HD (it was the only option). Now when I reboot the computer boots OS X automatically, but now I have no way of booting Ubuntu from my flash drive. I am able to run Ubuntu live from another flash drive by pressing option and selecting EFI boot, but I cannot boot my installation.

I booted the Live USB and mounted the EFI partition on my built in SSD and was surprised to see two folders within EFI/EFI: APPLE, and ubuntu (see screenshot). So it appears that the Ubuntu installer did install a bootloader on my SSD, but now my question is how would I select the ubuntu one if I want to boot Ubuntu?
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