Could someone give instructions (or a shell script) on how to convert ROMs under Linux?

Welcome to Omnimaga bwang. I don't have a shell script, but I would be happy to give you instructions on how to do this(I might make a shell script in a bit, was thinking about it before but never got around to it).

What you need:
TI-Boy SE(of course )
Wabbitsign(need wine): Epic Linkage
A GameBoy Rom

After you have all that, throw wabbitsign into your 'makeapp' directory. Open up your terminal and 'cd' to your 'makeapp' directory. Then type in what you see below:
cat 1.bin >> app.bin
echo -n "MyGBName" >> app.bin
cat 2.bin >> app.bin
cat your_rom.gb >> app.bin
cat 3.bin >> app.bin
wine ./wabbitsign.exe app.bin makeapp.8xk
rm ./app.bin

Please keep in mind, the name you place in the 'echo' has to be exactly 8 characters long, or it will not compile and of course replace 'your_rom.gb' with the rom you wish to convert

I'll whip up a script to automate this process and make life easier, until then you'll have to use this  way.

I hope this helps =D