Source tree compilation on Debian/Ubuntu

These binaries can also be used to run a local UCSC genome browser mirror.

Please note the instructions and scripts in the source tree that can build the kent source tree on any Linux system: src/product

These commands compile the UCSC genome browser and all source tools on Debian Lenny (64 and 32bit), Ubuntu Maverick and Ubuntu 13.04. They will put all binaries in /usr/local, all cgi-bins in /usr/lib/cgi-bin and all html-like things into /var/www/genome.

In theory, once you have installed the samtools library, you can just copy-paste this script into a command line

# we need to be root to install packages and put stuff into /usr/local
su 
# install required packages from repository
# please not that these won't install the samtools library to handle bam files
apt-get install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev libssl-dev openssl mysql-client-5.5  mysql-client-core-5.5
# set variables for compilation
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'
# this does not seem to be necessary anymore
#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  

cd ../jkOwnLib
make 

# compile browser
cd ..
make $DIRS

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

Add the parameter HG_WARN=-w to DIRS if you don't want the compilation to stop on error messages. Dirty, but it works. :-)