Installing Locally

This section details how to set ImmuneDB up locally on a machine. This is a more complicated process than using the Docker method but may be useful if you plan on running ImmuneDB remotely on a server rather than locally.

Dependency Installation


ImmuneDB utilizes MySQL as its underlying data store. We recommend using its drop-in replacement, MariaDB. Please consult their website and your operating systems package manager for installation instructions.

R (optional)

Baseline can optionally be used 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.

For genotyping, TIgGER must also be installed.

Bowtie2 (optional)

Bowtie2 can be used to locally align sequences which cannot be aligned using the built-in anchor method.

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

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

To create a virtual environment and activate it run:

$ virtualenv immunedb
$ source immunedb/bin/activate

Then install ImmuneDB

$ pip install immunedb