ImmuneDB
v0.29.0

Getting Started

  • Introduction
  • Installing with Docker (recommended)
    • Pulling the Docker Image
    • Running the Container
      • Next Steps
  • Installing Locally (advanced)

Running the Pipeline

  • Running the Example Pipeline
  • Running the Pipeline on Your Data

Querying an Existing Database

  • Python API
  • Directly Querying the Database

Other

  • Referencing ImmuneDB
  • Related Publications & Software
ImmuneDB
  • Docs »
  • Installing with Docker (recommended)
  • Edit on GitHub

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:v0.29.0

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:v0.29.0

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

Next Steps¶

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

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© Copyright 2018, Drexel University Systems Immunology Lab Revision dd8faf48.

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