Homer Software and Data Download

Installing Circos for use with HOMER can be divided into 3 parts. If you already use Circos on your system, you may only need to pay attention to the last part. I recommend checking out the official Circos installation directions. Below is a quick guide with tips:

1. Download the Circos software and unzip it into a location where you won't delete it.

You want to download the general circos package (i.e. circos-0.62-1.tgz). Save it to location, and unzip it (tar zxvf circos-0.62-1.tgz). (At this point you can also do step 3, which is add the circos bin/ directory to you executable PATH.

2. Upgrade your Perl modules to include the necessary prerequisites for Circos.

Follow the instructions on this page: Perl and Modules. It talks a little while as some of the modules will want to install dependencies. For the most part, this means running the command:

sudo perl -MCPAN -e shell

Followed by commands to install each missing module:
cpan[1]> install Config::General

The following modules need to be installed:

Config::General
GD
GD::Polyline
List::MoreUtils
Math::Bezier
Math::Round
Math::VecStat
Params::Validate
Readonly
Regexp::Common
Set::IntSpan
Text::Format
Font::TTF::Font
Clone

By far the trickiest part is installing GD - often, you need to install the system C libraries for GD. This often means running something like:

Linux (Ubuntu): "sudo apt-get install lib-gd2"
Linux (Redhat/CentOS): " yum install gd-devel"
Mac OSX: "sudo fink install gd2".

Try to follow the Circos instructions. Hopefully, buy the time you read this, it will be magically easier.

3. Add the Circos bin directory to you executable path so that you can run it by simply typing "circos" in the command line. (i.e. edit your ~/.bashrc or ~/.bash_profile file to include "PATH=$PATH:/Users/chucknorris/circos-0.54/bin/")