Installing Locally (recommended)¶
This section details how to set ImmuneDB up locally on a machine.
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
innodb_large_prefix = ON innodb_file_format = Barracuda
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 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