To compile bootstrap yourself the following steps have to be done:
1) You need an arm-gcc standalone compiler. The delivered arm-linux-gcc won't work for that task. Good ones are obtainable at http://www.codesourcery.com/
2) Extract the archive from your CD or from our download section (http://www.armbedded.eu/downloads) on your development PC. Change to that directory.
3) Edit the Makefile in the directory at91bootstrap to point the variable CROSS_COMPILE to your installed stand-alone cross-compiler, e.g.:

CROSS_COMPILE=/develop/arm-2008q3/bin/arm-none-eabi-

4) Now issue make in the at91bootstrap directory with the following options:

	make CHIP=at91sam9g20   BOARD=at91sam9g20-ek   ORIGIN=nandflash   DESTINATION=sdram   BIN_SIZE=0x30000   FROM_ADDR=0x20000   DEST_ADDR=0x23F00000   OP_BOOTSTRAP=on STR_DESCR=\\\"appli\\\" TRACE_LEVEL=1

5) Now you find your binary in at91bootstrap/bin directory:

boot-at91sam9g20-ek-nandflash2sdram.bin

. Bootstrap has to be flashed via SAM-BA. It cannot be flashed with u-boot or linux. To do that see this how-to: http://www.armbedded.eu/node/8