Docker/container overview

A container is quite similar to a virtual machine, and can be used to contain and execute all the software required to run a particular program or set of programs. The container includes an operating system (typically some flavor of Linux), plus a...
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Docker tutorial: Custom cloud environments for Jupyter notebooks

This is a step-by-step guide for 1) building and publishing a custom Docker image and 2) running a Jupyter Notebook on Terra using a Docker image modified to include additional packages. Contents 1. Clone the Git repository with the base images2. ...
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Install Docker and test that it works

Contents Get and install the software Test that the program runs Identify yourself Get an image and run a container Troubleshooting 1. Get and install the software Follow the relevant link below depending on your computer system; on Mac and Win...
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Run GATK in a Docker container

This document explains how to install and use Docker to run GATK on a local machine. For a primer on what Docker containers are for and related terminology, see this Dictionary entry. Contents Install Docker Test that it works Get the GATK conta...
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Working with project-specific environments in Terra

Compute environments allow you to launch different Terra-supported applications like Jupyter Notebooks or RStudio from your workspace. From your workspace cloud environments menu, you can select one of multiple pre-configured compute environments,...
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Creating safe and secure custom Docker images

If you are bringing your own Docker image, please consider the following security advisory If you are basing your image on anything other than Terra Base Images,  you have to decide whether you trust the provider of the image. Even if you think it...
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Make a Docker (container) image the easy way: using a base image

A Docker is a "container" - a software package including code and all its dependencies - designed to run applications quickly and reliably from one computing environment to another. By eliminating problems that arise when different people use diff...
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Publish a Docker container image to Google Container Registry (GCR)

This document explains how to create and utilize a public or private Google Container Registry (GCR) Docker image from inside FireCloud. This guide is useful for migrating or mirroring existing images from other repositories such as DockerHub. For...
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Accessing previous versions of Terra Jupyter notebook Docker images using the Google Container Registry

You can set up your Cloud Environment software by selecting a pre-configured Terra Docker image. Although these images are routinely updated to include the latest analysis software for your Jupyter Notebook applications,  you can still access an o...
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Selecting prior notebook cloud environment/application configurations versions

If you’re using Jupyter Notebooks on Terra, you should be aware of the fact that the pre-configured environments that are available to you through the Terra interface are regularly updated, and that you have several options when it comes to select...
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