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.
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.
For genotyping, TIgGER must also be installed.
Bowtie2 can be used to locally align sequences which cannot be aligned using the built-in anchor method.
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