SUSE Linux notes: Difference between revisions
From genomewiki
Jump to navigationJump to search
m (shell comand conenvtions) |
m (typo) |
||
Line 1: | Line 1: | ||
The usual conventions apply: | The usual conventions apply: | ||
* command issued from a root shell: <code># <command> </> | * command issued from a root shell: <code># <command> </code> | ||
* command issued from a user shell: <code>$ <command> </> | * command issued from a user shell: <code>$ <command> </code> | ||
= Prerequisites = | = Prerequisites = |
Revision as of 21:32, 15 May 2012
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
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}
- do integrity check on databases:
# mysqlcheck --all-databases