Source tree compilation on Debian/Ubuntu: Difference between revisions
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These commands compile the UCSC genome browser and all source tools 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. | These commands compile the UCSC genome browser and all source tools 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. | ||
<pre> | <pre> | ||
# we need to be root to install packages and put stuff into /usr/local | |||
su | su | ||
aptitude install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev | aptitude install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev | ||
# | # set variables for compilation | ||
export MYSQLLIBS="-lmysqlclient -lz" | export MYSQLLIBS="-lmysqlclient -lz" | ||
export MACHTYPE=$(uname -m) | export MACHTYPE=$(uname -m) | ||
export MYSQLINC=/usr/include/mysql | 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' | 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 | # download | ||
Revision as of 00:12, 30 January 2011
These commands compile the UCSC genome browser and all source tools 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.
# we need to be root to install packages and put stuff into /usr/local su aptitude install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev # 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 ../hg make $DIRS # set permissions cd /home/data/www chown apache:apache -R *
