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INSTALLATION

        These installation instructions assume being able to open and use a
        terminal window on Linux.
    
        (0) Some systems need several dependencies installed ahead of time.
    
            You may be able to skip this step. However, if subsequent steps don't
            work, then be sure that some basic libraries are installed, as shown
            below (or ask a system administrator to take care of it). For the
            applicable distribution, open a terminal and then type the commands as
            indicated:
    
            For RedHat or CentOS 5.x systems (tested on CentOS 5.5)
    
                    sudo yum install gcc
    
            For RedHat or CentOS 6.x systems (tested on "Minimal Desktop" CentOS 6.0)
    
                    sudo yum install gcc
                    sudo yum install perl-devel
    
            For Ubuntu systems (tested on Ubuntu 12-04 LTS)
    
                    sudo apt-get install curl
    
            For Debian 5.x systems:
    
                    sudo apt-get install gcc
                    sudo apt-get install make
    
        (1) Install the non-Perl dependencies:
            (Versions shown are those that we've tested. Please contact us if
            newer versions do not work.)
    
            Infernal            1.0.2    (http://infernal.janelia.org/)
            MAFFT               6.849b   (http://mafft.cbrc.jp/alignment/software/)
            RNA Vienna package  1.8.4    (http://www.tbi.univie.ac.at/~ivo/RNA/)
    
            After installing these, make sure all of the foloowing executables are
            in directories within your PATH:
    
                cmbuild
                cmcalibrate
                cmsearch
                cmalign
                mafft
                RNAalifold
    
        (2) Use a CPAN client to install Bio::App::SELEX::RNAmotifAnalysis.
    
            Here we demonstrate the use of cpanminus to install it to a local Perl module directory. These instructions assume absolutely no experience with cpanminus.
    
                  1. Download cpanminus
    
                        curl -LOk http://xrl.us/cpanm
    
    
                  2. Make it executable
    
                        chmod u+x cpanm
    
    
                  3. Make a local lib/perl5 directory (if it doesn't already exist)
    
                        mkdir -p ~/lib/perl5
    
    
                  4. Add relevant directories to your PERL5LIB and PATH environment
                     variables by adding the following text to your ~/.bashrc
                     file:
    
    
                        # Set PERL5LIB if it doesn't already exist
                        : ${PERL5LIB:=~/lib/perl5}
    
                        # Prepend to PERL5LIB if directory not already found in PERL5LIB
                        if ! echo $PERL5LIB | egrep -q "(^|:)~/perl5/lib/perl5($|:)"; then
                            export PERL5LIB=~/lib/perl5:$PERL5LIB;
                        fi
    
                        # Prepend to PATH if directory not already found in PATH
                        if ! echo $PATH | egrep -q "(^|:)~/perl5/bin($|:)"; then
                            export PATH=~/bin:$PATH;
                        fi
    
    
                  5. Update environment variables immediately
    
                        source ~/.bashrc
    
    
                  6. Install Module::Build
    
                        ./cpanm Module::Build
    
    
                  7. Install Text::LevenshteinXS (even if you already have it installed elsewhere)
    
                        ./cpanm Text::LevenshteinXS
    
    
                  8. Install Bio::App::SELEX::RNAmotifAnalysis
    
                        ./cpanm Bio::App::SELEX::RNAmotifAnalysis
    
    
        Please contact the author if, after consulting this documentation and
        searching Google with error messages, you still encounter difficulties
        during the installation process.

INCOMPATIBILITIES

        Windows:     lacks necessary *nix utilities
        SGI:         problems with compiled dependency Text::LevenshteinXS
        Sun/Solaris: problems with compiled dependency Text::LevenshteinXS
        BSD:         problems with compiled dependency Text::LevenshteinXS

BUGS AND LIMITATIONS

         There are no known bugs in this module.