I did this in Windows, but something similar can definitely be changed to run in *nix environments.
I was having issues with the Singe 2 keybindings not reading my controls.cfg so, I installed Hypseus and with a few modifications and tweaks I got All of the games setup within a couple of hours of work.
The end goal was to have it launch the Batch File from LaunchBox, but it had to run JoyToKey as a separate command, then start the hypseus in a normal sequence, but when it exits it kills the JoyToKey executable so as not to interfere with other games if I switch to a non-laser disc title.
Example of a batch file for Time Traveler
start <Path To JoyToKey>\JoyToKey.exe
ping -n 2 127.0.0.1>NUL
hypseus.exe singe vldp -framefile singe\timetraveler\timetraveler.txt -script singe\timetraveler\timetraveler.singe -fullscreen -volume_nonvldp 5 -volume_vldp 20 -js_range 5
Taskkill /IM JoyToKey.exe /F
EXIT
I ran JoyToKey (v6.5 at the time of writing) and setup a profile for "Hypseus"
Edit: Buttons were just pressed and highlighted what ones I wanted to set to what default. I had the default ini file open that tells you what key is what, and that's what I set it to in JoyToKey. Very straight forward.
In the profiles association in JoyToKey I setup the profile to link to where my Hypseus was installed to so it would switch automatically as they are different than the DaphneSinge that I still use for the original Dragon's Lair:
I also set one up for DaphneSinge so that the buttons were mapped accordingly:
All you have to do is add the ROMs using the Import Wizard, and select the batch file for the Hypseus and as long as your data files are in the appropriate folders, the batch file above will function inside the same directory that the hypseus.exe executable resides.
The line: ping -n 2 127.0.0.1>NUL
Is there for a 'delay' because I found that while I had JoyToKey running in the foreground, it will go in front of the game because it loads slower ever so slightly sometimes, and the game does not get focus. So I added it there. You can change JoyToKey to run minimized in the settings and delete that line if you wish.