Cloud Environment FAQs

The article shares some of the frequently asked questions about the interactive analysis cloud environment functionality in Terra. Please leave a comment on the article if you have more questions.  Frequently Asked Questions Do I have a differen...
See more

Understanding and adjusting your Cloud Environment

(Interactive applications - such as Jupyter Notebooks and Galaxy - run on virtual machines or clusters of machines in your Cloud Environment. When running an interactive application in Terra, you can adjust the configuration of the your Cloud Envi...
See more

What packages are installed on preconfigured Cloud Environments?

Learn how to check what packages are pre-installed on any of the application configurations in the Cloud Environments widget. You can also see a list of everything that's present on our base docker images for these environments here.   To check wh...
See more

Using a startup script to launch a pre-configured cloud environment

If the default environments available in the Application Configuration dropdown menu found in the Cloud Environments widget don't come with all of the packages you consistently need, and you'd like a more efficient way of launching a Jupyter noteb...
See more

Detachable Persistent Disks

Terra attaches a persistent disk (PD) to your Cloud Environment VM where you can store data (such as generated data and installed libraries) even if you delete or update your Cloud Environment. PDs also act as a safeguard to protect your data in ...
See more

Using the terminal and interactive analysis shell in Terra

With Terra's terminal interface you can execute UNIX command-line code quickly within the cloud environment that runs notebooks in a workspace. This allows you to perform actions like listing files, moving files to and from the notebook disk and a...
See more

Changing data file directories

UPDATE Oct 22, 2019: We were able to simplify how users need to change the file paths in notebooks that point to local data files. Therefore, the article below differs slightly from the email notification you may have received on October 18,2019. ...
See more

Viewing IGV tracks of BAM files in your workspace data

This article explains two ways you can use the Integrative Genomics Viewer (IGV) to examine tracks from BAM (.bam) files in Terra. From the workspace Data tab From the IGV web app 1. From the workspace Data tab Data files in the cloud linked to...
See more

Using the Bioconductor Docker image in Terra

The Bioconductor Docker image is one of the current base images integrated into Terra. This guide will introduce you to the Terra Bioconductor image and how to use it with a Jupyter Notebook.  Contents Introduction to Bioconductor and the Terra B...
See more

Launching seqr through Terra

Seqr is an open source web interface to make research productive, accessible, and user-friendly for medical researchers working on rare diseases genomics. It's a portal for searching through genomic data of rare diseases that provides information ...
See more

Getting started with GPUs in a Cloud Environment

A graphics processing unit (GPU) is optimized for linear algebra computations, such as matrix multiplication. Terra now supports the use of GPUs when using Jupyter notebook cloud environments. This feature is currently in beta, and you should be a...
See more

Preventing runaway costs with Cloud Environment autopause

To prevent runaway charges when no computational work is being done in a cloud environment, they will automatically pause when there is no web browser or kernel activity for 30 minutes. Note that kernel activity will only prevent autopause for up ...
See more

Adjusting autopause for Cloud Environments using Swagger

Occasionally, you may need to extend the default autopause time (30 minutes) to accommodate long-running (i.e. more than 24 hours) jobs. Note that autopause is already disabled for up to 24 hours as long as the kernel is running.  To do this witho...
See more

Saving data from an interactive environment to your workspace bucket

Saving data from an interactive cloud environment (such as an instance of RStudio, or a Jupyter notebook) is a useful trick in some situations. If you're worried about losing work that you've done in an interactive environment because you need to ...
See more

Protecting data from an old Cloud Environment

1. Identify notebooks in old clusters To see what Cloud Environments you created under each billing project, and when you created them, go to https://app.terra.bio/#clustersSee a virtual machine or cluster created before August 1st, 2020? Note the...
See more

Creating a custom cloud environment runtime with the Swagger API

To create a cloud environment runtime with non-default settings that aren't exposed through the Terra UI. In such cases, use the Swagger UI. Swagger lets you directly access the Leonardo API (Terra's interactive analysis API responsible for things...
See more

Accessing workspace data tables using AnVIL's R package

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) package includes a variety of functions written in R that are meant to enable users to do things like work with Terra/AnVIL table and data resources directly...
See more

Wrapping R scripts in WDL

This article provides some resources for those interested in running R scripts within their WDL code. The video below explains the steps of creating Docker files with the necessary dependencies for your R scripts, and how to run those R scripts fr...
See more