Installing with Docker (recommended)

Pulling the Docker Image

With Docker installed, run the following command to pull the newest version of the ImmuneDB Docker image:

$ docker pull  ghcr.io/arosenfeld/immunedb

Running the Container

To start a shell session within the container run:

$ docker run -v $HOME/immunedb_share:/share \
    -p 8080:8080 -it arosenfeld/immunedb

This will start a shell with ImmuneDB and accessory scripts pre-installed as well as create a shared directory between the host and Docker container. Files placed in the host’s $HOME/immunedb_share directory and it will appear in /share within the Docker container (and vice versa). Note $HOME on macOS is generally /Users/your_username/ and on Linux it is generally /home/your_username.

Additionally, MySQL stores its data in /share/mysql_data so databases will persist across multiple container invocations.

The location of important files are:

• /root/germlines: IMGT aligned germlines for IGH, TCRA, and TCRB.

• /apps/bowtie2/bowtie2: The local-alignment tool Bowtie2. This file is in the container’s $PATH.

• /share/configs: The recommended directory to store ImmuneDB configurations generated by immunedb_admin create.

• /share/mysql_data: The location MySQL (specifically MariaDB) will store its data.

• /example: A set of example input data to familiarize yourself with ImmuneDB.

Running ImmuneDB

Once the Docker container is running, you should continue by testing out the example pipeline.