NAME:     LocTree3
FUNCTION: predict protein subcellular localization
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 LocTree3
    cd software
    wget -c https://codeload.github.com/Rostlab/LocTree3/zip/develop -O LocTree3-develop.zip
    unzip LocTree3-develop.zip

#step3: Install LocTree3
    cd LocTree3-develop
    aclocal && autoconf && autoheader; automake --add-missing
    ./configure --prefix=/datadisk/PPVED-1.0/software/LocTree3-develop/install   #note: modify '/datadisk/PPVED-1.0' to your own path
    make && make install
    cd install/bin
    you may need to install Perl module 'Config::IniFiles' and List::Util' in advance, see the end of the file to learn how to install Perl module
    open script 'loctree3', and comment out its line 29, that is, add a character # before line 29
    echo "export PATH=/datadisk/PPVED-1.0/software/blast:\$PATH" >> ~/.bashrc   #note: modify '/datadisk/PPVED-1.0' to your own path
    source ~/.bashrc
    echo -e "[NCBI]\nData=/datadisk/PPVED-1.0/software/blast/" > ~/.ncbirc   #note: modify '/datadisk/PPVED-1.0' to your own path

#step4: test LocTree3
    cp ../share/doc/loctree3/examples/arch/arch_example.fa .
    cp ../share/doc/loctree3/examples/arch/arch_example.lc3 .
    ./loctree3 -i ./ -r arch_output.lc3 -d arch

    #results: the output file 'arch_output.lc3' should be identical to the provided file 'arch_example.lc3'.

    Congratulations, the installation is complete !



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

1. Install module 'Config::IniFiles'
    first, check whether the module 'Config::IniFiles' exists:
        perldoc Config::IniFiles
    if it does not exist, install it:
        wget -c https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Config-IniFiles-3.000003.tar.gz
        tar zxvf Config-IniFiles-3.000003.tar.gz
        cd Config-IniFiles-3.000003
        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 'Config::IniFiles' is installed normally
        perldoc Config::IniFiles

2. Install module 'List::Util'
    first, check the version of the module 'List::Util':
        perl -e 'use List::Util; print $List::Util::VERSION, "\n"'
    if it is 1.27, install it:
        wget -c https://cpan.metacpan.org/authors/id/P/PE/PEVANS/Scalar-List-Utils-1.55.tar.gz
        tar zxvf Scalar-List-Utils-1.55.tar.gz
        cd Scalar-List-Utils-1.55
        #yum install -y perl-devel
        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/x86_64-linux-thread-multi:\$PERL5LIB" >> ~/.bashrc   #note: if you modify '/root/perllib/install', you should also modify it here
        source ~/.bashrc
    finally, check the version of the module 'List::Util':
        perl -e 'use List::Util; print $List::Util::VERSION, "\n"'