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

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

  • set up the environment
    • tip: use two different shells (one user shell, one root shell) with (very) different colorschemes in parallel
    • user shell:$ source env_variables
    • root shell:# source env_variables
    • you will switch between both, so you should operate on a common ground
  • create CGI directory:$ mkdir -p ${CGI_BIN}-${USER}
  • set the naive file permissions:# chmod 777 ${CGI_BIN}-${USER}
  • create all directories as needed:
mkdir -p ${SAMDIR}
mkdir -p ${TABIXDIR}
mkdir -p ${DOCUMENTROOT}
mkdir -p ${CGI_BIN}
mkdir -p ${TRASHDIR}
mkdir -p ${KENTBIN}
mkdir -p ${BINDIR}
mkdir -p ${SCRIPTS}

build from source

  • build and install ncurses:
tar -xf ncurses-5.9.tar.gz
cd ncurses-5.9
./configure
make
make install.libs DESTDIR= /genome/src/ncurses/
cd ..
rm -rf ncurses-5.9
  • build and install samtools:
mkdir -p ${SAMDIR}
wget http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2
tar -xf samtools-0.1.18.tar.bz2
cd samtools-0.1.18
wget http://genomewiki.ucsc.edu/images/7/7f/Knetfile_hooks.0.1.18.patch
patch -p1 < Knetfile_hooks.0.1.18.patch
    • edit in Makefile the variable LIBPATH
    • set to LIBPATH= -L/genome/src/ncurses/usr/lib
mkdir -p ${SAMDIR}
make
cp -r samtools-0.1.18/* ${SAMDIR}
cd ..
rm -rf samtools-0.1.18
  • build and instal tabix:
tar -xf tabix-0.2.5.tar.bz2
cd tabix-0.2.5
wget http://genomewiki.ucsc.edu/images/e/e8/Knetfile_hooks_tabix-0.2.5.patch
patch -p1 < Knetfile_hooks_tabix-0.2.5.patch
    • edit in Makefile the variable LIBPATH
    • set to LIBPATH= -L/genome/src/ncurses/usr/lib
mkdir -p ${TABIXDIR}
make
cd ..
cp -r tabix-0.2.5/* ${TABIXDIR}
rm -rf tabix-0.2.5
  • get the browser source via git: $ git clone http://genome-source.cse.ucsc.edu/kent.git
  • build the source: $ cd kent/src and run $ make
    • clang instead of gcc also works
  • check size of htdocs (around 452.45M):$ rsync -nahvz --progress --stats rsync://hgdownload.cse.ucsc.edu/htdocs
  • get production copy of html docs: $ rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ $WEBROOT/

the database

  • start MySQL: # service mysql start
  • check for right database:# mysql -u root -p mysql_root_password -e "show databases;" | grep ${GENOME}
  • do integrity check on databases: # mysqlcheck --all-databases

see also