As you may be aware, every single docker run command creates a new container and executes a command specified in the Dockerfile, CMD, or ENTRYPOINT. The running container will have its own file system, networking stack, and isolated process tree separate from the host. To spin-up a container from an image, you need to use the docker run command. If you are a more “video person”, you may want to check this video, which covers the same topics of this article. Note: The tag isn't there at all it's been replaced by the digest, which is a more specific identifier.In this guest tutorial by Jaroslaw Krochmalski, the author of “ Docker and Kubernetes for Java Developers”, you’ll learn how to run and stop Docker containers manually from the shell or the command line.īefore getting started, you may want to check my book “ 5 Steps to an extraordinary career“, which will guide you to build your dream career as a software developer! Click here to check it out. Once you have the RepoDigests, you write in your WDL. The one you want is the "RepoDigests" one, not the "Id". Note: In the latter case, there are two things that look like sha256:something_long. "RepoDigests": a lot of other details we don't care about right now. The digest will be displayed in the output as: Digest: sha256:96bf2261d3ac54c30f38935d46f541b16af7af6ee3232806a2910cf19f9611ce If the image is on your computer Type docker pull my_repo/my_image:tag at the prompt. The result you want will look something like sha256:something_long, where the something_long bit is the digest. In both cases, you'll work in the terminal app. There are two ways to get the digest for my_repo/my_image:tag. For example, if you want private images to be used in Docker Hub, add "firecloud" as a Collaborator so that it can pull the private image. If you're concerned about privacy, access to Docker images can be set through the registry. Ensuring security and privacy when working in the cloud By referencing Docker images in a workflow configuration, anyone in the workspace can launch the same analysis without worrying about whether they are using the exact same environment or downloading the right applications. Workflows in FireCloud use Docker to distribute tools and applications. The other way to use Docker is on a cloud-based platform, like FireCloud. For a concrete example, see this tutorial. Once the container is running, you can run any software inside it that is installed on its system. Then you tell it to initialize the container, which is equivalent to booting up a virtual machine. One way to use Docker is on your laptop: First, you tell the docker program to download a container image (= a file) from a registry (e. There are others, like Dockstore, which is specifically geared toward bioinformatics, and GCR, which is Google's general-purpose container registry for use on Google Cloud. Docker Hub is where Broad teams publish most of their Docker images here). Another way to distinguish between an image and a container is to think of the image as a snapshot of the container that isn't running.Īn image can be distributed through one or more registries, which are repositories where users can store images privately or publicly in the cloud. You know how sometimes when you need to install new software on your computer, the download file is called a "disk image"? That's because the file you download is in a format your operating system treats as if it was a physical disk on your machine. Note: This has nothing to do with pictures here the word "image" is used in the same software-specific way that refers to a special type of file. ![]() How to build and store containers with images and registriesĪ container is packaged as an image. However, docker with a lowercase "d" is also the command-line program that you install on your machine to run Docker containers. ![]() Sometimes we say "a docker" instead of "a container" - similar to how "xerox" became a verb for "to copy" due to the dominance of the Xerox company. There are other brands, such as Singularity, but Docker is the most popular and widely used. It can be run as a self-contained virtual environment, making it easier to reproduce the same analysis on any infrastructure that supports running the container without having to go through the pain of identifying and installing all the software dependencies on your own laptop, cluster, or cloud environment.ĭocker is one of several brands of container systems. The container includes an operating system (typically some flavor of Linux), plus any required software installed on top of the OS. A container is similar to a virtual machine (VM) and can be used to contain and execute all the software required to run a particular program or set of programs.
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