Requirements
Once you understand the requirements, continue to the installation documentation.
UNIX vs Windows
If you are a Windows users, read how how Circos differes on UNIX and Windows.
Perl
You will need Perl to run Circos. Perl is an interpretive language, like Python or Ruby. It is available for nearly every operating system and if you're on UNIX or Mac OS X, you very likely already have it installed.
Perl 5.8.x, or newer, is recommended.
You can download Perl from perl.org, or as a package for your operating system from your vendor or distributor. Windows users are encouraged to try Strawberry Perl.
Modules
Additional code contributed by the Perl community (modules) is required to run Circos. You can obtain all the modules from CPAN.
In addition to the core modules that already ship with Perl, refer to the list of required modules.
For a full list of modules, run
> cd bin > ./list.modules
To test whether you have each module
> cd bin > ./test.modules
True Type Fonts
Your version of the GD module must be compiled with support for True Type fonts. This is normally the case, but if you find that your images do not have any text on them, this is because your version of GD does not include TTF support. You'll need to reinstall GD, making sure that you have the True Type library (freetype) first installed on your system.
Bitmap fonts
For small text, bitmapped fonts are best - you can find many free fonts at DaFont.
The Mini font set is an attractive alternative.
These fonts are in True Type format, but have been designed to be displayed at a fixed resolution. This is achieved by the font's designer by restricting each letter to a fixed pixel matrix and designing the font by toggling individual pixels. Bitmap fonts are typically not antialiased (no subpixel sampling, which smooths the edges) in order to maintain legibility at small sizes.
Keep in mind that because bitmap fonts are not designed to be anti-aliased, they don't render well when rotated.