SUSE Linux notes

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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

build from source

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