You need to allow the user running the web server a read access to both MPQ files of StarCraft. These files are stardat.mpq and broodat.mpq and can be found in any StarCraft installation. They MUST be renamed in lower case, otherwise the minimap generation will fail. The directory to these files will be the first parameter to provide in each minimap generation function.
On Unix, it's a good idea to have libpeg around ; otherwise, you'll have to modify the Makefiles so that RepASM outputs BMPs instead of JPEG. For Windows binaries, it's already included in the DLL.