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INSTALL  view on Meta::CPAN

    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';

    if you used the second method. By doing this, the installed modules are
    found by your program. To run the runDiscovery.pl program, you would
    need to do

       perl -I/home/lib/perl5/site_perl/5.16.3 runDiscovery.pl

       or

       perl -I/home/lib

    Of course, you could also add the 'use lib' line to the top of the
    program yourself, but you might not want to do that. You will need to
    replace 5.8.3 with whatever version of Perl you are using. The preceding
    instructions should be sufficient for standard and slightly non-standard
    installations. However, if you need to modify other makefile options you
    should look at the ExtUtils::MakeMaker documentation. Modifying other
    makefile options is not recommended unless you really, absolutely, and
    completely know what you're doing!

    NOTE: If one (or more) of the tests run by 'make test' fails, you will
    see a summary of the tests that failed, followed by a message of the
    form "make: *** [test_dynamic] Error Y" where Y is a number between 1