GET STARTED

• Before you start
• Cloud infrastructure pricing
• Developer dashboard
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TUTORIALS

• Quickstart - TCGA data (controlled access required)
• Quickstart (open data)
• Comprehensive user guide
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GUIDES

• Collaborating on the CGC: A Guide for Consortia
• Using CGC for Workshops and Courses
• Secure Configuration Guide

ACCESS THE CGC

• Sign up for the CGC
• Access via the visual interface
• Access via the API
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MANAGE AN ANALYSIS ENVIRONMENT

• Projects on the CGC
• Create a project
• View a project
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MANAGE FILES

• Overview
• File repositories on the CGC
• Copy files using the visual interface
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BRING DATA TO THE CGC

• Upload your data to the CGC
• Upload from your computer
• Upload via the command line
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COLLABORATE SECURELY

• Collaboration on the CGC
• Add a collaborator to a project
• Set permissions

DATASETS HUB

• ABOUT DATASETS
• About data access
• TCGA data
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PUBLIC PROJECTS

• Public projects overview
• Smart Variant Filtering
• Cancer Cell Line Encyclopedia (CCLE)
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SET METADATA ASSOCIATED WITH A PRIVATE FILE

• Metadata for your private data
• System metadata
• Metadata schema
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FIND APPS

• Apps on the CGC
• Workflows and tools
• Interactive Web Apps

BRING YOUR TOOLS

• About the SDK
• About the Common Workflow Language
• CWL v1.0 improvements over sbg:draft-2
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TOOL WRAPPING TIPS AND TRICKS

• Make files available in your tool's working directory
• Set the default value for an input port
• JavaScript Cookbook
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DOCKER

• About Docker
• Install Docker
• The CGC Image Registry
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DESCRIBE YOUR TOOL (LEGACY)

• The Tool Editor
• General Tool Information
• Tool Input Ports
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EDIT AN APP (LEGACY)

• Copy public apps to a project
• Copy an app from a project
• Edit a tool
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ARCHIVE APPS

• App archiving overview
• Archive an app
• Restore an app

RUN AN ANALYSIS

• About analyses
• Run a task
• Define app settings
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TASK EXECUTION

• About task execution
• About controlling task execution
• About parallelizing tool executions
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REVIEW A TASK

• Review the task page
• View Task stats
• View Task logs
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VIEW ANALYSIS RESULTS

• View output files

INTERACTIVE ANALYSIS

• Interactive analysis on the CGC
• Seven Bridges Genome Browser
• Variant Browser
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DOWNLOAD RESULTS

• Download results

DEVELOPER TOOLS

• Developer Hub
• Get your authentication token
• Publish your app in the Public Apps gallery

CONNECT CLOUD STORAGE

• Connect cloud storage overview
• About Volumes
• About aliases
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API Hub

• API Overview
• API Quickstart
• Using volumes via the API
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API CLIENTS

• Store credentials to access Seven Bridges client applications and libraries
• R library
• Client libraries
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SB Command Line Interface

• Seven Bridges Command Line Interface
• General commands
• Billing
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EDIT AN APP

• About the editor
• The tool editor
• The workflow editor

ASYNC BULK ACTIONS

• Overview
• Copy multiple files
• Delete multiple files and folders
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WES API

• Overview
• Run a workflow
• Cancel a running workflow
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DATA STUDIO

• About Data Studio
• JupyterLab quick reference
• RStudio quick reference
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SBFS (Beta)

• About SBFS
• Install SBFS manually
• Install SBFS automatically
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SBFS Command Reference

• Overview
• Configure
• List
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