Chanjo targets Unix and Python 2.7+/3.2+. Since chanjo relies on Sambamba for BAM processing, it’s now very simple to install. I do still recommend Miniconda, it’s a slim distribution of Python with a very nice package manager.

$ pip install chanjo

Vagrant dev/testing environment

You can also set up a local development environment in a virtual machine through Vagrant. This will handle the install for you automatically through Ansible provisioning! After downloading/cloning the repo:

$ vagrant up
$ vagrant ssh


You will also need a copy of Sambamba which you can simply grab from their `GitHub repo`_ where they serve up static binaries - just drop the latest in your path and you are good to go!

$ wget -P /tmp/
$ tar xjfv /tmp/sambamba_v0.5.8_linux.tar.bz2 -C /tmp/
$ mv /tmp/sambamba_v0.5.8 ~/bin/sambamba
$ chmod +x ~/bin/sambamba

Optional dependecies

If you plan on using MySQL for your SQL database you also need a SQL adapter. My recommendation is ‘pymysql’. It’s written in pure Python and works on both version 2.x and 3.x.

$ pip install pymysql

Getting the code

Would you like to take part in the development or tweak the code for any other reason? In that case, you should follow these simple steps and download the code from the GitHub repo.

$ git clone
$ cd chanjo
$ pip install --editable .