Docker

Docker is a platform for developing, shipping, and running applications in isolated environments.

The key components are:

• Container: A lightweight, standalone, executable package that includes everything needed to run a piece of software
• Image: A read-only template with instructions for creating a container, built from layers
• Dockerfile: A text file containing commands to build a Docker image automatically
• Registry: A repository for Docker images (like Docker Hub)
• Volume: A persistent storage space shared between host and container
• Network: Enables containers to communicate with each other and external resources

Dockerfile

Dockerfile example:

FROM rocker/shiny:latest
RUN apt-get update
RUN apt-get install -qq -y libpq-dev
RUN install2.r ggplot2 shiny shinydashboard \
    shinydashboardPlus \
    dplyr RPostgres

Explanation:

• FROM specifies the base image
• RUN executes a command in the container

Basic Docker Commands

Description	Command
Start application	docker run <container-name/container-id>
List containers	docker ps
List docker images	docker images
Pull images from registry	docker pull
Kill container	docker kill <container-name/container-id>
Build image based on Dockerfile	docker build <dir-with-docker-file>
Execute command inside container	docker exec <command> <container>

Interacting with Containers

Start a container and execute bash:

docker run -d rocker/shiny
docker exec -it rocker/shiny /bin/bash

Start R directly in a container:

docker exec -it rocker/shiny /usr/local/bin/R

Container Management

Description	Command
Stop container	docker stop <container-name/container-id>
Remove container	docker rm <container-name/container-id>
Remove container and its volumes	docker rm -v <container-name/container-id>
Restart container	docker restart <container-name/container-id>

Docker Compose

Docker Compose is a tool for defining and running multi-container Docker applications using a YAML file. Example docker-compose.yml:

services:
  postgres:
    container_name: db_container
    build: ./postgres
    restart: always
    environment:
      - POSTGRES_USER=postgres
      - POSTGRES_PASSWORD=postgres
    ports:
      - "5432:5432"
    volumes:
      - "./pgdata:/var/lib/postgresql/data"
  
  shiny:
    container_name: shiny
    depends_on:
      - postgres
    build: ./shiny
    volumes:
      - "./shiny-logs:/var/log/shiny-server"
      - "./shiny-home:/srv/shiny-server"
    ports:
      - "3838:3838"

Run docker-compose:

docker compose up --force-recreate

Debugging Tips

View container logs:

docker logs <container-name>

Prevent container from crashing for debugging: Add to docker-compose.yml:

command: "sleep infinity"

Container Status

Description	Command
List running containers (with grep filter)	docker ps \| grep <container-name>
Show all containers including stopped ones	docker ps -a

Container Logs:

Description	Command
View container logs	docker logs <container-name>
Follow container logs live	docker logs -f <container-name>
Show last N lines of logs	docker logs --tail=100 <container-name>

Network Debugging:

Description	Command
Check port mappings	netstat -tulpn | grep <port-number>
Test container connectivity	curl -v http://localhost:<port>
List all Docker networks	docker network ls
Inspect network settings	docker network inspect <network-name>

Container Information:

Description	Command
Show detailed container info	docker inspect <container-name>
Show container resource usage	docker stats <container-name>
Show processes running in container	docker top <container-name>

Troubleshooting Commands:

Description	Command
Check if container can reach internet	docker exec <container-name> ping 8.8.8.8
Get shell access inside container	docker exec -it <container-name> /bin/bash
Check container logs since specific time	docker logs --since 30m <container-name>
Check container environment variables	docker exec <container-name> env

Volume Inspection:

Description	Command
List volumes	docker volume ls
Inspect volume	docker volume inspect <volume-name>
Check volume mount points	docker inspect -f '{{ .Mounts }}' <container-name>