Getting Started (Bare Metal)

This section details how to set ImmuneDB up locally on a machine. Alternatively, you can use Docker Compose to get up and running more quickly.

Dependency Installation

MySQL

ImmuneDB utilizes MySQL as its underlying data store. As it is a drop-in replacement for MySQL, MariaDB can also be used and is recommended. Please see the associated website for installation instructions.

You must set the following variables under the [mysqld] header in your MySQL configuration (by default found at /etc/mysql/my.cnf):

innodb_large_prefix = ON
innodb_file_format = Barracuda

Baseline & R (optional)

ImmuneDB can use Baseline to calculate selection pressure on clones. This requires R to be installed along with the ade4 package. Installation is platform dependent.

The newest version of Baseline can be downloaded here. The path to the main script will be needed for clone statistics generation as described in Statistics Generation.

Clearcut (optional)

Clearcut can be used to generate lineage trees for clones. After downloading and compiling per the instructions, note the path to the clearcut executable which will be required for generating trees in Clone Trees (Optional).

ImmuneDB Installation

virtualenv

It is recommended that ImmuneDB be installed within a virtual environment, creating an isolated environment from the rest of the system.

If virtualenv package is not installed, install it globally with:

$ sudo pip install virtualenv

Then create and activate a new virtual environment where NAME should be replaced with an appropriate name:

$ virtualenv NAME
$ cd NAME
$ source bin/activate

Finally, get and install ImmuneDB:

$ pip install numpy
$ pip install immunedb

Global

Warning

Installing many packages globally is not recommended. Using virtual environments keeps dependencies separated from the root filesystem. Only in specialized situations (e.g. within a VM) should ImmuneDB installed globally.

If instead a global install is desired, run:

$ pip install numpy
$ pip install immunedb