INSTALLATION 

Prerequisites

Function2Gene requires the following modules and programs to work
properly:

  * perl
  * wget
  * HTML::TreeBuilder
  * HTML::ElementTable
  * XML::Parser

The operating system-specific instructions below will help you to
install these modules.

Unix instructions

If you're running a reasonably modern Linux (or other UNIX variant,
like MacOS X) you already have perl and wget. If so, you can install
the remaining modules by doing the following:

 cpan install HTML::TreeBuilder
 cpan install HTML::Element::Extended
 cpan install XML::Parser

If you are running Debian, you can just run the following:

 aptitude install wget perl libhtml-element-extended-perl libxml-parser-perl

Windows

If you are using a windows-based machine, first consider switching to (or
dual-booting) Debian or Ubuntu or a similar Free Software distribution. If
switching isn't for you, you will need to install cygwin (a linux-like
environment for windows), which (by default) will install perl and wget.

You can then use the cpan commands listed above to install the required
modules:

 cpan install HTML::TreeBuilder
 cpan install HTML::Element::Extended
 cpan install XML::Parser

Other Operating Systems

If you are using another operating system (minux, MacOS 9, UNIVAX, Plan9,
OS/2, etc.) you're on your own.


USAGE

All of the programs are located within a bin directory. For a
demonstration, you can simply do the following:

cd bin;
echo 'transferrin' > keywords.txt
function2gene --keywords keywords.txt --results keyword_results;