NAME:     NetPhos 3.1
FUNCTION: predict protein phosphorylation 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 NetPhos
    cd software
    #you need an academic application to get the download address of NetPhos (https://services.healthtech.dtu.dk/service.php?NetPhos-3.1)
        e.g. : you got a download address https://services.healthtech.dtu.dk/download/6819b825-dd2e-41e9-a66b-86eb7a49f949/netphos-3.1.Linux.tar.Z
    wget -c https://services.healthtech.dtu.dk/download/6819b825-dd2e-41e9-a66b-86eb7a49f949/netphos-3.1.Linux.tar.Z
    tar zxvf netphos-3.1.Linux.tar.Z

#step3: Install NetPhos
    cd ape-1.0
    modify lines 21, 25, 28, 31 and 49 of file 'ape', and the modified contents look like this:
        line 21 = setenv  APE     /datadisk/PPVED-1.0/software/ape-1.0
        line 25 = setenv  ARCH    i386
        line 28 = setenv  TMP     /datadisk/PPVED-1.0/software/ape-1.0/tmp
        line 31 = setenv  MAXCPU  8
        line 49 = setenv PYTHON /usr/bin/python

#step4: test NetPhos
    cp ../testdata/test.fa .
    cp ../testdata/test.netphos .
    ./ape test.fa >test.output

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

    Congratulations, the installation is complete !