NAME:     SCRATCH 1.2
FUNCTION: predict protein secondary structure and relative solvent accessibility
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 SCRATCH
    cd software
    wget -c http://download.igb.uci.edu/SCRATCH-1D_1.2.tar.gz
    tar zxvf SCRATCH-1D_1.2.tar.gz

#step3: Install SCRATCH
    cd SCRATCH-1D_1.2/pkg
    mv blast-2.2.26 blast-2.2.26-old
    wget -c ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
    tar zxvf blast-2.2.26-x64-linux.tar.gz
    cd ..
    perl install.pl   #note: you may need to install Perl module 'ExtUtils::MakeMaker' and 'Env' in advance, see the end of the file to learn how to install Perl module

#step4: test SCRATCH
    cd doc
    ../bin/run_SCRATCH-1D_predictors.sh test.fasta test.out 4

    #results: the four output files (test.out.ss, test.out.ss8, test.out.acc, test.out.acc20) should respectively
    be identical to the provided files (test.hom.ss, test.hom.ss8, test.hom.acc, test.hom.acc20).

    Congratulations, the installation is complete !



================================================
Here is to teach you how to install Perl module
================================================

1. Install module 'ExtUtils::MakeMaker'
    first, check whether the module 'ExtUtils::MakeMaker' exists:
        perldoc ExtUtils::MakeMaker
    if it does not exist, install it:
        wget -c https://cpan.metacpan.org/authors/id/B/BI/BINGOS/ExtUtils-MakeMaker-7.58.tar.gz
        tar zxvf ExtUtils-MakeMaker-7.58.tar.gz
        cd ExtUtils-MakeMaker-7.58
        perl Makefile.PL INSTALL_BASE=/root/perllib/install   #note: 'INSTALL_BASE' is used to specify the installation path of the module, so you can modify '/root/perllib/install' to any position you want
        make
        make test
        make install
        echo "export PERL5LIB=/root/perllib/install/lib/perl5:\$PERL5LIB" >> ~/.bashrc   #note: if you modify '/root/perllib/install', you should also modify it here
        source ~/.bashrc
    finally, check whether module 'ExtUtils::MakeMaker' is installed normally
        perldoc ExtUtils::MakeMaker

2. Install module 'Env'
    first, check whether the module 'Env' exists:
        perldoc Env
    if it does not exist, install it:
        wget -c https://cpan.metacpan.org/authors/id/F/FL/FLORA/Env-1.04.tar.gz
        tar zxvf Env-1.04.tar.gz
        cd Env-1.04
        perl Makefile.PL INSTALL_BASE=/root/perllib/install   #note: 'INSTALL_BASE' is used to specify the installation path of the module, so you can modify '/root/perllib/install' to any position you want
        make
        make test
        make install
        echo "export PERL5LIB=/root/perllib/install/lib/perl5:\$PERL5LIB" >> ~/.bashrc   #note: if you modify '/root/perllib/install', you should also modify it here
        source ~/.bashrc
    finally, check whether module 'Env' is installed normally
        perldoc Env