Docker

Overview

Docker packages software and all of its dependencies into a portable container image that runs identically on any machine. The BioContainers project maintains Docker images for most bioinformatics tools, giving you single-command access to pre-built, version-locked binaries.

Docker is best suited for local workstations and cloud VMs. For shared HPC clusters see Singularity / Apptainer.

Installation

Install Docker Engine following the official instructions for your platform:

Linux – https://docs.docker.com/engine/install/
macOS – https://docs.docker.com/desktop/install/mac-install/
Windows (WSL 2) – https://docs.docker.com/desktop/install/windows-install/

Verify the installation:

docker --version
docker run hello-world

Basic Usage

Pulling and running a BioContainers image

# Pull and run a Docker image for FastQC
docker pull biocontainers/fastqc:v0.12.1
docker run --rm -v $(pwd):/data biocontainers/fastqc:v0.12.1 \
  fastqc /data/sample_R1.fastq.gz /data/sample_R2.fastq.gz

# BioContainers provides images for most bioinformatics tools
# See: https://biocontainers.pro

--rm removes the container after it exits. -v $(pwd):/data mounts your current directory into the container at /data so that input files are visible and output files are written back to the host.

Running an interactive shell

docker run --rm -it -v $(pwd):/data biocontainers/samtools:v1.19 bash

This drops you into a shell inside the container where samtools is available.

Key Parameters

`docker run`

Flag	Description
`--rm`	Automatically remove the container when it exits.
`-v host:container`	Bind-mount a host directory into the container.
`-it`	Allocate a pseudo-TTY and keep stdin open (interactive mode).
`-w`	Set the working directory inside the container.
`--cpus`	Limit CPU cores (e.g. `--cpus 4`).
`--memory`	Limit memory (e.g. `--memory 8g`).
`-e`	Set an environment variable inside the container.

`docker image`

Command	Description
`docker images`	List downloaded images.
`docker image rm <image>`	Delete a local image to free disk space.
`docker system prune`	Remove all stopped containers, unused networks, and dangling images.

Expected Output

After running the FastQC container, the host directory will contain:

sample_R1_fastqc.html
sample_R1_fastqc.zip
sample_R2_fastqc.html
sample_R2_fastqc.zip

Open the HTML files in a browser to inspect quality metrics.