SUSE Linux notes: Difference between revisions
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= Prerequisites = | = Prerequisites = | ||
== Software == | |||
* sources to download | * sources to download | ||
** [http://www.gnu.org/software/ncurses/ncurses.html ncurses] | ** [http://www.gnu.org/software/ncurses/ncurses.html ncurses] | ||
| Line 6: | Line 7: | ||
*** [http://sourceforge.net/projects/samtools/files/tabix/ tabix] | *** [http://sourceforge.net/projects/samtools/files/tabix/ tabix] | ||
== other == | |||
* environment variables | * environment variables | ||
export KENTHOME=$HOME/kent | export KENTHOME=$HOME/kent | ||
Revision as of 21:27, 15 May 2012
Prerequisites
Software
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
