NAME:     DIpro 2.0
FUNCTION: predict protein disulfide bond
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 DIpro
    cd software
    wget -c http://download.igb.uci.edu/dipro2.0.tar.gz
    tar zxvf dipro2.0.tar.gz

#step3: Install DIpro
    install SSpro 4.0
        wget -c http://download.igb.uci.edu/sspro4.tar.gz
        tar zxvf sspro4.tar.gz
        cd sspro4
        open script 'configure.pl', and set the '$install_dir' (line 24) to the sspro4 installation directory
            e.g. : $install_dir = "/datadisk/PPVED-1.0/software/sspro4/";
        ./configure.pl
        mv blast2.2.8 blast2.2.8-old
        mkdir blast2.2.8
        cd blast2.2.8
        wget -c ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.8/blast-2.2.8-amd64-linux.tar.gz
        tar zxvf blast-2.2.8-amd64-linux.tar.gz
    install DIpro
        cd ../../dipro2.0
        open script 'configure.pl', and set the DIpro path ($install_dir, line 19) and SSpro4 path ($pspro_dir, line 22) to their installation directories
            e.g. : $install_dir = "/datadisk/PPVED-1.0/software/dipro2.0/";
            e.g. : $pspro_dir = "/datadisk/PPVED-1.0/software/sspro4/";
        ./configure.pl
    set the search path of shared library files
        echo "export LD_LIBRARY_PATH=.:\$LD_LIBRARY_PATH" >> ~/.bashrc
        source ~/.bashrc
        chmod 755 ../../library/ld-linux.so.2
        cp ../../library/ld-linux.so.2 /lib   #note: you need root permission, please ask the server administrator to help you

#step4: test DIpro
    cd test
    cp ../../../library/lib*.so.? .
    ../bin/predict_disu.sh seq1.fasta seq1.output

    #results: the output file 'seq1.output' should be identical to the provided file 'test1.disu'.

    Congratulations, the installation is complete !