SUSE Linux notes

The usual conventions apply:

• command issued from a root shell: # <command>
• command issued from a user shell: $ <command>

Prerequisites

Software

• sources to download
  • ncurses:$ wget http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz
  • SAMtools
    • SAMtools:$ wget http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2
    • tabix:$ wget http://downloads.sourceforge.net/project/samtools/tabix/tabix-0.2.5.tar.bz2
• software from the repositories
  • libmysqlclient-devel
  • mysql-community-server
  • mysql-community-server-tools
  • libpng14-devel
  • apache2
  • git
• install via: # zypper install libmysqlclient-devel mysql-community-server mysql-community-server-tools libpng14-devel apache2 git

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

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

• Build Environment Variables
• openSUSE