SUSE Linux notes
From genomewiki
The usual conventions apply:
- command issued from a root shell:
# <command> - command issued from a user shell:
$ <command>
Prerequisites
Software
- sources to download
- software from the repositories
- libmysqlclient-devel
- mysql-community-server
- mysql-community-server-tools
- libpng14-devel
- apache2
- install via:
# zypper install libmysqlclient-devel mysql-community-server mysql-community-server-tools libpng14-devel apache2
other
- environment variables (file env_variables):
export KENTHOME=$HOME/kent
export USE_BAM=0
export SAMDIR=/genome/src/samtools/samtools-0.1.18
export SAMINC=${SAMDIR}
export SAMLIB=${SAMDIR}/libbam.a
export USE_TABIX=1
export TABIXDIR=/genome/src/tabix/tabix-0.2.5
export TABIXINC=${TABIXDIR}
export TABIXLIB=${TABIXDIR}/libtabix.a
export KNsETFILE_HOOKS=1
export MACHTYPE=`uname -m`
export MYSQLINC=/usr/include/mysql
export MYSQLLIBS="-L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib -L/usr/lib64 -lssl -lcrypto"
export MYSQLDATA="/var/lib/mysql"
export DOCUMENTROOT=/var/www/html-$USER
export WEBROOT=$DOCUMENTROOT
export CGI_BIN=/var/www/cgi-bin
export KENTBIN="$KENTHOME/bin"
export BINDIR="${KENTBIN}/$MACHTYPE"
export SCRIPTS="${KENTBIN}/scripts"
export TRASHDIR="/var/www/trash"
export ENCODE_PIPELINE_BIN="${BINDIR}"
export AUTH_MACHINE="genome"
export AUTH_USER=$USER
export GLOBAL_CONFIG_FILE=${CGI_BIN}/hg.conf
export HGCGI=$CGI_BIN
Installation process
- set up the environment:
$ source env_variables - create CGI directory:
$ mkdir -p ${CGI_BIN}-${USER} - tip: use two different shells (one user shell, one root shell) with (very) different backgrounds in parallel
build from source
- get the source via git:
$ git clone http://genome-source.cse.ucsc.edu/kent.git
the database
- start MySQL:
# mysql -u root -p mysql_root_password -e "show databases;" | grep ${GENOME} - do integrity check on databases:
# mysqlcheck --all-databases
