Circos is a software tool that lets you make beautiful circular figures, which are increasingly a common feature of genome-related papers (here are some examples). Circos, which is free to use, is built on Perl and requires a lot of Perl modules to be installed in order to work.

This is not always as straightforward as one might imagine, though Circos helps you by providing a tool to quickly see which modules you already have and which still need to be installed. I've previously set up Circos on Mac OS X, but today I had to install it on our Linux box (running CentOS 6). These are the steps I went through in order to get Circos up and running. Hopefully, this might be useful to others in the same situation.

### Installing Circos on CentOS ###

# These instructions assume that you are installing Circos in 
# a '/Bioinformatics/Packages' directory and also that you have root access

# Preparatory steps
su
mkdir /Bioinformatics/Packages/Circos
cd /Bioinformatics/Packages/Circos


# Download the latest *.tgz release and copy to Circos directory
wget http://circos.ca/distribution/circos-0.64.tgz
tar -xvzf circos-0.64.tgz
cd circos-0.64


# To test what modules we will need to install, use Circos' built-in tool
cd bin
./test.modules


# This leads to having to install:
perl -MCPAN -e 'install Clone'
perl -MCPAN -e 'install Config::General'
perl -MCPAN -e 'install Font::TTF::Font'
perl -MCPAN -e 'install GD'

# GD module installation failed and so I had to to also install gd library:
yum install gd gd-devel


# now back to the Perl modules
perl -MCPAN -e 'install GD'
perl -MCPAN -e 'install List::MoreUtils'
perl -MCPAN -e 'install Math::Round'
perl -MCPAN -e 'install Math::VecStat'
perl -MCPAN -e 'install Params::Validate'

# Params::Validate didn’t seem to install properly, so I tried a manual approach
cd
wget http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Params-Validate-1.07.tar.gz
tar -xvzf Params-Validate-1.07.tar.gz
cd Params-Validate-1.07
perl Build.PL

# This failed because I needed a newer version of some other Perl modules
# even though the ./test_modules script reported everything was okay
perl -MCPAN -e 'install Module::Build'
perl -MCPAN -e 'install Module::Implementation'


# Can now hand install Params-Validate
./Build
./Build test
./Build install

# And back to the Perl modules
perl -MCPAN -e 'install Readonly'
perl -MCPAN -e 'install Regexp::Common'
perl -MCPAN -e 'install Text::Format'


# Tidy up and set up symbolic links
rm -rf ~/Params-Validate-1.07
rm ~/Params-Validate-1.07.tar.gz
cd /Bioinformatics/Packages/Circos
ln -s circos-0.64 current
cd /Bioinformatics/bin
ln -s ../Packages/Circos/current/bin/circos

# Try running circos
./circos

# This still wasn’t enough!!!
# Running circos complained that I needed 2 more Perl Modules!
perl -MCPAN -e 'install Math::Bezier'
perl -MCPAN -e 'install Set::IntSpan'

# Try running circos again
./circos

# Success! And by 'success' I mean that you can now get to a point where you are
# seeing errors from the Circos program (i.e. you need to set up your Circos
# configuration file).