Circos, the Perl-package for visualizing data and information in a circular layout is an immensely popular application in the bio-informatics/bio-visualization community. And rightly so, as it able to produce visually stunning and appealing graphics.
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…