Because its the native environment is bio-informaticians, the software is written in Perl. For those without Perl experience, it can be slightly frustrating to set it up on OSX (as it was for me). Here are the steps I needed to do to get it running, hope that this might reduce the trouble and let others get to work on their visualization more quickly.

The whole installation process is also detailed on the Installation page.

1 Getting Circos
Download the software, tutorials, tools and courses

2 Testing the modules
Go the the circosX-XX/bin folder and run: ./test.modules
This gives you a list of the installed Perl modules, and – more importantly – the ones still missing.

3 Install the missing modules
Switch to the super user with ‘su’.
For each missing modules say: cpan -i Modulename::Subname

cpan -i Config::General
cpan -i Graphics::ColorObject
cpan -i Math::VecStat
etc, etc

All worked swimmingly, except GD was making a bit of trouble.

4 Installing GD
The graphics library GD has to be present on your system. If it’s not, install it. (I am with homebrew, therefore installing GD is done like that: brew install gd)

Still after installing GD, installing the Perl module would not work. But after applying a little force, it went fine:

cpan -i -f GD

5 Adding circos to your path
Adding the circos ‘bin’ directory to your path lets you call the circos program directly without specifying the whole path. That’s a good thing.

PATH="/path/to/circos-0.55/bin:${PATH}"
export PATH

After that, everything should work and your Circos adventure can begin…

$command = "perl /my/perl/script.pl";
$results = exec($command);
// does not print error

If the perl script generates error, you won’t be able to see them, as they are written to stderr.

One solution might be to append the stderr to stdout, therefore getting it into the $results variable.

$command = "perl /my/perl/script.pl 2>&1";
$results = exec($command);
// Prints: Died at /my/perl/script.pl line 25.

As this post explains, 1 means stdout, 2 means stderr. 2>1 might look ok at first sight, but the ’1′ will be interpreted as a filename. Therefore it has to be escaped with &1, resulting in 2>&1.