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Create and upload a Docker image

Overview

In order to use your own tools on the Seven Bridges Platform, you need to install each tool in an individual Docker image, and then upload the image to the Seven Bridges Image Registry or to Docker Hub.

Prerequisites

Before you can create and upload a Docker image, you need to install Docker. You also need to make sure Docker is running, as follows:

  • Mac OS 10.10.3 Yosemite or newer: run Docker for Mac and start a terminal of your choice.
  • Mac OS 10.8 Mountain Lion or newer: run Docker Quickstart terminal to start Docker Machine.
  • Windows 10: run Docker for Windows and start a terminal of your choice.
  • Windows 7 or 8: run Docker Quickstart Terminal to start Docker Machine.
  • Linux: no action required.

Steps

To create and upload a Docker image:

  1. Run docker login images.sbgenomics.com and enter your Seven Bridges credentials. Don't forget: enter your authentication token when prompted for a password.

📘

If you are using the Seven Bridges Platform on AWS EU, please use eu-images.sbgenomics.com as the image registry instead of images.sbgenomics.com.

  1. Open a Docker base image.
  2. Install your tool in the image.
  3. Commit your image.
  4. Push your image to the Seven Bridges registry.

Open a Docker image

If you are installing a tool, you'll need to start from a base image. On the other hand, if you are modifying a tool that you have already uploaded, you can pull the image containing the tool from the Seven Bridges registry.

To install a tool, start from a base image. This can be any base image from Docker Hub, but starting with a plain operating system image like Ubuntu is generally recommended. To use this base image, enter:

docker run -ti ubuntu

To pull an image from the Seven Bridges registry, enter the repository that the image is stored in, followed by the image tag (if any), separated by a colon. The full repository path has the format images.sbgenomics.com/<username>/<repository_name>[:tag]. For example, if the user rfranklin wanted to open the image tagged 1.3 from her picard repository, she would enter

docker-run -ti images.sbgenomics.com/rfranklin/picard:1.3

Install your tool inside a Docker container

Inside a container you can install your chosen tool or modify an existing tool. Do this in the way that you would normally, using methods appropriate for your tool, e.g. apt-get. Files from the local host can be accessed in the directory /mountedcwd. So, if the software you want to install is stored in a remote repository, you can git pull your code and mount it into the container.

When you've finished installing a tool, leave the container by typing exit.

Commit your image

After you exit the container, you can commit the image of it.
First, list all your local containers, so that you can commit an image (snapshot) of the ubuntu container that you just created. The -a option here lists all containers, include those that are not currently running; you should see a container that was just created recently. This is the one you want.

$ docker ps -a

CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS                      PORTS               NAMES

c52b82b497eb        ubuntu              "/bin/bash"              2 minutes ago       Exited (0) 2 minutes ago                        kickass_liskov
ae194ed75819        debian              "/bin/bash"              7 hours ago         Exited (0) 7 hours ago                          jovial_swanson
34ff1377fbee        hello-world         "/hello"                 26 hours ago        Exited (0) 26 weeks ago                         high_almeida
54240578230c        c0bfb9c8e377        "/bin/sh -c '/usr/gam"   26 hours ago        Exited (0) 26 weeks ago                         serene_pare
517904a42f3d        docker/whalesay     "cowsay hhLinked Appl"   27 hours ago        Exited (0) 27 weeks ago                         romantic_bhaskara
1aad55d740cd        docker/whalesay     "cowsay docker/whales"   27 hours ago        Exited (0) 27 weeks ago                         cocky_bhaskara
7bfb18e0d18a        hello-world         "/hello"                 28 hours ago        Exited (0) 28 weeks ago                         stupefied_williams

👍

Your local containers

If you have followed the Docker Quickstart, on their website, or used Docker in any other way, you might have already created some containers. You should see those listed too.

Grab the CONTAINER ID of the ubuntu image that was created 2 minutes ago. It's c52b82b497eb.
Now, we'll commit an image of that container. This also gives you the opportunity to name your image. You must name it with the format images.sbgenomics.com/<username>/<repository_name>[:tag]. For example, if the user rfranklin wanted to commit her changes to a container in a repository named picard, with tag 1.4 she would name the image images.sbgenomics.com/rfranklin/picard:1.4.

Commit the image as follows:

$ docker commit c52b82b497eb images.sbgenomics.com/rfranklin/picard:1.4

If you want to confirm that the image has been named, you can list all of your local images.

$ docker images 

REPOSITORY                                TAG                 IMAGE ID            CREATED             VIRTUAL SIZE

images.sbgenomics.com/rfranklin/picard    1.4                 0fe5d1d1aaec        10 minutes ago      125.1 MB
rfranklin/test                            latest              0fe5d1d1aaec        18 minutes ago      125.1 MB
debian                                    latest              7a01cc5f27b1        7 hours ago         125.1 MB
ubuntu                                    latest              6cc0fc2a5ee3        8 months ago        187.9 MB
hello-world                               latest              0a6ba66e537a        8 months ago        960 B
docker/whalesay                           latest              ded5e192a685        8 months ago        247 MB

Push your image

To push your image to the Seven Bridges image registry, run the command docker push images.sbgenomics.com/<username>/<repository_name>[:tag], where <username>/<repository_name>[:tag] refers to the image that you have already committed. For example:

$ docker push images.sbgenomics.com/rfranklin/picard:1.4
The push refers to a repository [images.sbgenomics.com/rfranklin/picard] (len: 1)
[email protected]: pushed
1.4: digest: sha256:afc9023f29719ffd361cdcbc334fe4ec2c041997ee501a15a86ed7f6e9277008 size: 3990

The progress of the image upload will be shown in the terminal. When it has completed, you will see the message pushed.

Delete a local Docker image

If you want to delete a Docker image, use docker rmi images.sbgenomics.com/<username>/<repository_name>[:tag]. For example:

$ docker rmi images.sbgenomics.com/rfranklin/picard:1
Deleted 02c8c0913b94a09053dccded886512b77fbd2ecbe18930d1b059bb573f13afd1

Updated about a year ago

Create and upload a Docker image


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