Doing Research on Terra

Overview

• What kind of analysis can you do on Terra?
• The Workspace: Organize data, organize and run analysis tools
• Finding data, analysis tools, and template workspaces in the Library
• Start with curated sample workspaces for a variety of use-cases

Controlling Cloud Costs

• Understanding and controlling cloud costs
• Controlling Cloud costs - sample use cases

All About Data

• Uploading to a workspace Google bucket
• Broad Genomics: Transferring data out of a Terra workspace
• Populating the Data table
• Where's the link for a file in a workspace Google bucket?
• Using "Requester Pays" workspaces/buckets
• Converting common genomics file formats

Processing Data with Workflows (aka Methods)

• Getting started with GATK workflows in the cloud FAQs
• Finding the workflow (method) you need in the Methods Repository
• Configure a workflow to process your data
• Troubleshooting errors in Job Manager
• CPUs and persistent disk quotas: What are they and how do you request more?
• Create and/or edit a new workflow

Interactive Analysis and Visualization (Jupyter Notebooks)

• Interactive analysis with Jupyter notebooks
• Viewing IGV tracks for BAM files in your workspace data
• Saving and transferring notebook data using Jupyter environment variables
• Notebooks 101: How not to lose data output files or collaborator edits
• Terra's Jupyter Notebooks environment Part I - Key components
• Terra's Jupyter Notebooks environment Part II: Key operations

See all 9 articles

Secure Collaboration

• How to share or clone a workspace
• Terra/FireCloud Security Posture

Working with Docker

• Making a Docker image the easy way: Using a base image
• Publishing a Docker container image to Google Container Registry