$Id: INSTALL,v 1.6 2006/12/06 14:17:35 sendu Exp $

bioperl-network Installation

1. Requirements
2. Installing bioperl-network (Unix or Cygwin)
3. Installing bioperl-network (Windows and ActiveState Perl)


1. Requirements 

    Perl 5.6.1 is required.

	The bioperl-network package depends on the core BioPerl package. See 
	http://www.bioperl.org/wiki/Getting_BioPerl or the BioPerl INSTALL file
	for instructions for downloading and installing BioPerl. You must
    install at least the corresponding version of Bioperl: since this
    is bioperl-network 1.5.2, bioperl 1.5.2 is required.
	
	bioperl-network also depends on Perl's Graph package. See CPAN at 
	www.perl.org for instructions on downloading and installing Graph,
	use Graph version .80 or greater.

	Reading PSI XML files using bioperl-network requires the XML::Twig 
	module. See CPAN at www.perl.org for instructions on downloading 
	and installing XML::Twig.


2. Installing bioperl-network (Unix, Mac OS X and Cygwin)

    Installation instructions at the following address apply here:
    http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
    The following sections summarize the essential points from there.

    Using CPAN:
    To install using CPAN you will need a recent version (v1.8802 has
    been tested) of it and your prefer_installer conf set to 'MB':
    
    >cpan
    cpan>o conf prefer_installer MB
    cpan>o conf commit
    cpan>q
    
    Now find the name of the bioperl-network version you want:

    >cpan
    cpan>d /bioperl-network/
    Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
    Distribution S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
  
    Now install:

    cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz

    If you've installed everything perfectly then you may pass all the tests
    run in the './Build test' phase.
    It's also possible that you may fail some tests. Possible explanations:
    problems with local Perl installation, previously undetected bug in
    Bioperl, flawed test script and so on. A few failed tests may not affect
    your usage of bioperl-network.

    If you decide that the failed tests will not affect how you intend to use
    bioperl-network and you'd like to install anyway do:

    cpan>force install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz

    This is what most experienced Bioperl users would do. However, if you're
    concerned about a failed test and need assistance or advice then contact
    bioperl-l@bioperl.org.
    
    
	Manual installation:
    >gunzip bioperl-network-<release-version>.tar.gz
    >tar xvf bioperl-network-<release-version>.tar
    >cd bioperl-network
    
    where <release-version> is the current release.
    
    >perl Build.PL
    
    You can run regression tests and install bioperl-network using the
    following commands:
    
    >./Build test  
    >./Build install


    You may have to have root privileges in order to run './Build install' 
    successfully on Unix. See the BioPerl INSTALL file for alternative approaches
    if you don't have root or administrative privileges.


3. Installing bioperl-network (Windows and ActiveState Perl)

    The following page on the BioPerl website has up-to-date
    instructions on how to install bioperl-network on Windows:

    http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

    (the instructions are aimed at bioperl-core, but apply
    equally to bioperl-network)