Source tree compilation on Debian/Ubuntu

This worked on Debian Lenny (64 and 32bit) and Ubuntu Maverick. It will put all binaries in /usr/local, all cgi-bins in /usr/lib/cgi-bin and all html-like things into /var/www/genome.

su 
aptitude install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev
# libmysqlclient.a does not contain SSL symbols, so use shared library
export MYSQLLIBS="-lmysqlclient -lz"
export MACHTYPE=$(uname -m)
export MYSQLINC=/usr/include/mysql
DIRS='SCRIPTS=/usr/local/bin CGI_BIN=/usr/lib/cgi-bin DOCUMENTROOT=/var/www/genome BINDIR=/usr/local/bin ENCODE_PIPELINE_BIN=/usr/local/bin'

# download
cd /usr/local
wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
unzip jksrc.zip
mkdir -p /var/www/genome/

# compile libraries
cd kent/src/lib
make compile $DIRS

cd ../jkOwnLib
make compile $DIRS

# compile browser
cd ../hg
make $DIRS

# set permissions
cd /home/data/www/hgw-max
chown apache:apache -R *