We'll use the amidi command which is part of the ALSA *) utilities package (alsa-utils on Debian). This is a very common package so it's probably already installed. Please refer to your Linux distribution documentation for instructions on how to install this package if it's not already available.
All commands can be run as an ordinary user; you don't have to be root.
Connect the Sub 37 to your computer using an USB cable, and enter the following command:
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amidi --list-devices
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Dir Device Name
IO hw:1,0,0 Moog Sub 37 MIDI 1
Next, just send the stepX.syx files to the Sub 37 one by one using the following commands. The result of each step will be exactly as described in the Update Instructions by Moog (included in the firmware release archive).
Substitute the "hw:1,0,0" part with your result from the first command. And for other firmware versions you'll need to use other filenames, of course.
-p designates to MIDI port to use, and -s tells it to send the mentioned file.
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amidi -p hw:1,0,0 -s sub37_1_1_0_step1.syx
amidi -p hw:1,0,0 -s sub37_1_1_0_step2.syx
amidi -p hw:1,0,0 -s sub37_1_1_0_step3.syx
amidi -p hw:1,0,0 -s sub37_1_1_0_step4.syx
After this your firmware will be updated.
*) ALSA is the Advanced Linux Sound Architecture, see http://www.alsa-project.org