SUSE Linux notes

The usual conventions apply:

• command issued from a root shell: # <command>
• command issued from a user shell: $ <command>

Prerequisites

Software

• sources to download
  • ncurses
  • SAMtools
    • SAMtools
    • tabix
• 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

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

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

see also

• Build Environment Variables
• openSUSE