NAME:     UbPred
FUNCTION: predict protein ubiquitination sites
NOTE:     assume that the path of PPVED is '/datadisk/PPVED-1.0'
================================================================

#step1: Change the current working directory to the path of PPVED
    cd /datadisk/PPVED-1.0

#step2: Download and decompress UbPred
    cd software
    mkdir UbPredDT
    cd UbPredDT
    wget -c http://www.ppved.org.cn/dependent/dependent_software/UbPredDTFileLinux.zip
    unzip UbPredDTFileLinux.zip

#step3: Install UbPred
    wget -c http://www.ppved.org.cn/dependent/other_programs/MCR.tar.gz
    tar zxvf MCR.tar.gz
    echo "export MCRHOME=/datadisk/PPVED-1.0/software/UbPredDT/MCR/v78" >> ~/.bashrc   #note: modify '/datadisk/PPVED-1.0' to your own path
    echo "export LD_LIBRARY_PATH=\$MCRHOME/runtime/glnx86:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export LD_LIBRARY_PATH=\$MCRHOME/bin/glnx86:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export LD_LIBRARY_PATH=\$MCRHOME/sys/os/glnx86:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export LD_LIBRARY_PATH=\$MCRHOME/sys/java/jre/glnx86/jre1.6.0/lib/i386:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export LD_LIBRARY_PATH=\$MCRHOME/sys/java/jre/glnx86/jre1.6.0/lib/i386/native_threads:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export LD_LIBRARY_PATH=\$MCRHOME/sys/java/jre/glnx86/jre1.6.0/lib/i386/server:\$LD_LIBRARY_PATH" >> ~/.bashrc
    echo "export XAPPLRESDIR=\$MCRHOME/X11/app-defaults" >> ~/.bashrc
    source ~/.bashrc
    chmod 755 UbPredDTFile
    cp ../../library/lib*.so.? .

#step4: test UbPred
    ./UbPredDTFile s.txt test.output
    dos2unix p.txt   #note: 'p.txt' is a file in windows format, which is converted to linux format here

    #results: the output file 'test.output' should be identical to the provided file 'p.txt'.

    Congratulations, the installation is complete !