Here is a excerpt from pocket heaven wiki.
Patching with Linux
"Patching commercial NDS ROMs with Supercard Software works with Linux on x86 based PCs using Wine. To install Wine on a Debian based Linux, open a shell and type sudo apt-get install wine . Then you can run Win32 applications using wine name_of.exe :
1. Install the Supercard Software: wine setupmicrosdV256en.exe
2. Start the patcher: wine SuperCardmicrosd.exe
This was tested using Ubuntu, Wine 0.9.22 and Supercard Lite Software v2.56. "