$Id$

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, but 5.8 or greater is recommended.

	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 should
   install at least the corresponding version of Bioperl: since this
   is bioperl-network 1.6, bioperl 1.6 or greater is recommended.
	
   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 .86 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 id = C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
  
   Now install:

    cpan>install C/CJ/CJFIELDS/BioPerl-network-1.6.0.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 C/CJ/CJFIELDS/BioPerl-network-1.6.0.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.
