1. Create a new directory for your Dockerfile
For example:
mkdir SVdownstream && cd SVdownstream
2. Create a new file in the directory named Dockerfile
touch Dockerfile
3. Choose a base image to start from
Add this to the first line of the Dockerfile. Some examples:
FROM rocker/rstudio:4.0.3
FROM python:3.8-slim
FROM ubuntu:20.04
4. Add any dependencies that your application needs
To work out what dependencies are needed, look at install scripts or Dockerfile templates provided by the tool's developer.
5. Configure any environment variables or other settings
To work out what is needed, look at install scripts or Dockerfile templates provided by the tool's developer.
6. Define any commands or entrypoints to run when the container starts
To work out what is needed, look at install scripts or Dockerfile templates provided by the tool's developer.
8. Build the image
For example:
sudo docker build -t <name>:<tagVersion> .
9. Build .sif with singularity
For example:
sudo singularity pull docker-daemon:containername:1.0
10. Upload to DockerHub
On the Dockerhub website, select Repositories and then Create repository
From the command line:
docker tag <local-image>:<tagVersion> <repo-name>:<tag-name>
docker push <new-repo>:<tag-name>
Build a docker image from a dockerfile:
docker build -t imagename:version . (or /path/to/dockerfile)
Run a docker container from an image:
docker run imagename
List all running docker containers:
docker ps
List all docker images:
docker images
Remove a docker image:
docker rmi imagename (or ID)
Clear docker cache. This command will remove all stopped containers, dangling images, unused networks, and build cache. Additionally, it will remove all volumes not used by at least one container. Note that this will permanently delete these items, so make sure you want to do this before running the command.
docker system prune -a --volumes