SUSE Linux notes: Difference between revisions

From genomewiki
Jump to navigationJump to search
(Category:Installation)
(mysql service start)
Line 33: Line 33:
  export GLOBAL_CONFIG_FILE=${CGI_BIN}/hg.conf
  export GLOBAL_CONFIG_FILE=${CGI_BIN}/hg.conf
  export HGCGI=$CGI_BIN
  export HGCGI=$CGI_BIN
* start MySQL: <code># mysql -u root -p mysql_root_password -e "show databases;" | grep ${GENOME}</code>


= see also =
= see also =

Revision as of 19:55, 15 May 2012

Prerequisites

  • 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
  • start MySQL: # mysql -u root -p mysql_root_password -e "show databases;" | grep ${GENOME}

see also