Installing with Docker (recommended)¶
Pulling the Docker Image¶
With Docker installed the following command to get the newest version of the ImmuneDB Docker image:
$ docker pull arosenfeld/immunedb:v0.29.3
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:v0.29.3
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 byimmunedb_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
Next Steps¶
Once the Docker container is running, you should continue by testing out the example pipeline.