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NAME
    ALBD Installation Guide

TESTING PLATFORMS
    ALBD has been developed and tested on Linux primarily using Perl.

SYNOPSIS
     perl Makefile.PL

     make

     make test

     make install

DESCRIPTION
    ALBD provides a system for performing ABC co-occurrence literature based
    discovery using a variety of options, and association-based ranking
    methods

REQUIREMENTS
    ALBD REQUIRES that the following software packages and data:

  Programming Languages
         Perl (version 5.16.3 or better)

  CPAN Modules
         UMLS::Association
         UMLS::Interface

  Required for some Methods:
         MATLAB
         MySQL (version 5 or better)

INSTALLATION STAGES
    The installation is broken into four stages:
    Stage 1: Install Programming Languages If already installed you need at
    minimum: - Perl version 5.16.3 or better
    Stage 2: Install CPAN Modules
    Stage 3: Install ALBD
    Stage 4: Create an co-occurrence matrix

  Stage 1: Install Programming Languages, if already installed go to Stage 2
    Perl (version 5.16.3 or better) Perl is freely available at
    <http://www.perl.org>. It is very likely that you will already have Perl
    installed if you are using a Unix/Linux based system.

  Stage 2 - Install CPAN modules, if already installed go to Stage 3
    If you have supervisor access, or have configured MCPAN for local
    install, you can install each of these via:

         perl -MCPAN -e shell
         > install <packageName>

   UMLS::Interface
    The core UMLS package provides a dictionary from content unqiue
    identifiers (CUI) to their meanings in the Unified Medical Language
    System. Refer to the UMLS::Interface documentation for how to install
    the UMLS database on your system.

    The package is freely available at:
    <http://search.cpan.org/dist/UMLS-Interface/>

   UMLS::Association
    Use to calculate association scores used in most of the ranking method.

    The package is freely available at:

        <http://search.cpan.org/dist/UMLS-Association/>

  Stage 3: Install ALBD package
    The usual way to install the package is to run the following commands:

        perl Makefile.PL
        make
        make test
        make install

    You will often need root access/superuser privileges to run make
    install. The module can also be installed locally. To do a local
    install, you need to specify a PREFIX option when you run 'perl
    Makefile.PL'. For example,

        perl Makefile.PL PREFIX=/home

        or
    
        perl Makefile.PL LIB=/home/lib PREFIX=/home

    will install UMLS-Interface into /home. The first method above will
    install the modules in /home/lib/perl5/site_perl/5.16.3 (assuming you
    are using version 5.16.3 of Perl; otherwise, the directory will be
    slightly different). The second method will install the modules in
    /home/lib. In either case the executable scripts will be installed in
    /home/bin and the man pages will be installed in home/share.

    Warning: do not put a dash or hyphen in front of PREFIX, or LIB

    In your perl programs that you may write using the modules, you may need
    to add a line like so

       use lib '/home/lib/perl5/site_perl/5.16.3';

    if you used the first method or

       use lib '/home/lib';