The Seven Bridges Knowledge Center

The Seven Bridges Platform is a simple solution for doing bioinformatics at industrial scale. But sometimes, everyone needs a little help.

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Core Docker commands

This section contains core Docker commands for running containers and pushing images to the Seven Bridges images registry.

First make sure Docker is running

  • 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.
Command
Effect

$ docker login images.sbgenomics.com

This returns a prompt for your Seven Bridges credentials, and then, if satisfied, gives you access to the Seven Bridges registry. Don't forget to add images.sbgenomics.com to this command, or else the utility will attempt to log you in to the Docker Hub registry.

You can enter your username in any of the following three ways:

  • In the same format as when logging in to the Platform (including uppercase, periods etc.).
  • In lower case, while replacing non-alphanumeric characters with underscores.
  • As the email address you used to register for the account on the Platform.

You should enter your authentication token in response to the password prompt, not your Seven Bridges password.

$ docker run -ti <image>

This runs a Docker container on your local machine. <image> can be any image in Docker Hub or the Seven Bridges image registry that you have uploaded or have permission to access. The -ti flag makes the container run, interactively.

If you are opening an image from Docker Hub, specify <image> using <Docker_repository>[:tag], e.g.ubuntu.
If you are opening an image from the Seven Bridges registry, <image> should be specified using the format images.sbgenomics.com/<user_name>/<project_name>/[:tag], e.g images.sbgenomics.com/rfranklin/samtools:v1.

$ docker ps -a

This lists all your Docker containers.

docker commit <container ID> images.sbgenomics.com/<repository>[:tag]

This takes an image (snapshot) of the container with ID <container ID>, and names the image with the format recognised by the Seven Bridges registry.
You can find the container ID of an image using docker ps -a.
Recall that <repository> has the form <user_name>/<project_name>.

$ docker images

This lists all your local Docker images.

$ docker tag <repository> images.sbgenomics.com/<repository>

This tags the image with a reference to
the Seven Bridges registry.

$ docker push images.sbgenomics.com/<repository> [:tag]

This uploads your Docker image to the Seven Bridges registry. , so that the tool in it can be used on the Platform.

$ docker rmi images.sbgenomics.com/<image name>

This removes the specified Docker image from your local machine. Typically image name will have the format <user_name>/<project_name>.

$ docker pull images.sbgenomics.com/<repository>[:tag]

This downloads the specified image from the Seven Bridges registry.

$ docker logout images.sbgenomics.com

This terminates your connection to the Seven Bridges image registry.

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/