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v1.0

Guides API Datasets Hub Release Notes CGC

Guides

v1.0Home Guides API Reference

GET STARTED

Before you start
Account settings
Cloud infrastructure pricing
Developer dashboard
About the Payments page
Email notifications page

TUTORIALS

Quickstart - TCGA data (controlled access required)
Quickstart (open data)
Comprehensive user guide
Worked example of uploading SamTools Sort
Upload a custom python program using a Dockerfile
Bring your own tools to the Cancer Genomics Cloud
Maintaining and versioning CWL on external tool repositories
Estimate and manage your cloud costs
Troubleshooting tutorial

GUIDES

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

ACCESS THE CGC

Sign up for the CGC
Access via the visual interface
Access via the API
Credits

MANAGE AN ANALYSIS ENVIRONMENT

Projects on the CGC
Create a project
View a project
Manage the project dashboard
Modify project settings
Restrict file downloads
Add notes to your project
Delete a project
Leave a project
Manage email notifications

MANAGE FILES

Overview
File repositories on the CGC
Copy files using the visual interface
Copy files using the API
Search files on the CGC
Tag your files
Activity center
File archiving overview
Import individual files (Copy DRS URI)
New File Browser

BRING DATA TO THE CGC

Upload your data to the CGC
Upload from your computer
Upload via the command line
Import from an FTP or HTTP(S) server
Upload via the API
Import from a Volume
Import data from the PDC
Import data from ICDC
Import data from the GC
Import from a DRS server
Import data from the GDC
Import data from the CTDC
Import data from Gen3 AnVIL to CGC
Dynamic PFB Importer

COLLABORATE SECURELY

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

DATASETS HUB

PUBLIC PROJECTS

Public projects overview
Smart Variant Filtering
Cancer Cell Line Encyclopedia (CCLE)
ICGC-TCGA DREAM Somatic Mutation Calling Challenge
Simons Genome Diversity Project (SGDP) dataset
The Cancer Imaging Archive (TCIA) project
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) project
Personal Genome Project UK (PGP-UK) pilot dataset
Human Cell Atlas Preview Datasets
Data Studio Interactive Analyses
Bulk RNA-Seq Transcription Profiling of HSV-1 Infected Cells
Cancer Data Aggregator (CDA) with CGC: Usage Guide
MCMICRO - End to End Microscopy Image Processing

SET METADATA ASSOCIATED WITH A PRIVATE FILE

Metadata for your private data
System metadata
Metadata schema
Edit metadata using the visual interface
Edit metadata with a manifest
Export metadata to a manifest
Edit metadata using the command line uploader
Edit metadata using the API
Metadata manifest file format
Generate DRS manifest

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
CWL v1.2 conditional execution
Bring Nextflow apps to the CGC
Bring WDL apps to the CGC
Bring your Shiny apps to the CGC

TOOL WRAPPING TIPS AND TRICKS

Make files available in your tool's working directory
Set the default value for an input port
JavaScript Cookbook
Set suggested input values for CWL v1.x apps

DOCKER

About Docker
Install Docker
The CGC Image Registry
Create and upload a Docker image
Create and upload a Docker image with a Dockerfile
Manage Docker repositories
Core Docker commands
Mount a USB drive in a Docker container

DESCRIBE YOUR TOOL (LEGACY)

The Tool Editor
General Tool Information
Tool Input Ports
Tool Output Ports
Additional Tool Information
Test the Tool Description
Dynamic Expressions in Tool Descriptions
Advanced features of the tool editor
Fork a tool

EDIT AN APP (LEGACY)

Copy public apps to a project
Copy an app from a project
Edit a tool
Create a workflow
Edit a workflow
Revision notes

ARCHIVE APPS

App archiving overview
Archive an app
Restore an app

RUN AN ANALYSIS

About analyses
Run a task
Define app settings
Set computation instances
Import Dockstore apps to the CGC
About batch analyses
About secondary (index) files

TASK EXECUTION

About task execution
About controlling task execution
About parallelizing tool executions
About tool resource requirements
About Memoization (Reuse)
Project and file locations (Multi-cloud)
Set execution hints at workflow level
Set execution hints at node level
Set execution hints at tool level
Set execution hints at task level
About Spot/Preemptible Instances
Use Spot/Preemptible Instances
List of execution hints
List of task statuses
List of available Amazon Web Services US East instances
List of available Google Cloud Platform instances
Estimate task costs (Cost estimator)

REVIEW A TASK

Review the task page
View Task stats
View Task logs
Job retry
View instance metrics
Real-time job monitoring
Troubleshoot a failed task

VIEW ANALYSIS RESULTS

View output files

INTERACTIVE ANALYSIS

Interactive analysis on the CGC
Seven Bridges Genome Browser
Variant Browser
CummeRbundQC RNA-Seq Visualization
FastQC
Picard Alignment Summary metrics
The Seven Bridges Coverage app
dbGaP Submission Form Suite

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
Access Volumes
Supported cloud storage providers
Amazon Web Services Simple Storage Service (AWS S3) Volumes
- Attach an Amazon Web Services (AWS) volume
- AWS Cloud storage tutorial
Google Cloud Storage (GCS) Volumes
- Attach a Google Cloud Storage volume
- Google Cloud Storage tutorial
Microsoft Azure Volumes
- Attach a Microsoft Azure volume
Enabling cross-origin resource sharing (CORS)
Security concerns when working with volumes
Manage members for a volume
Browse and add files to a project from a volume
Deactivate a volume

API Hub

API Overview
API Quickstart
Using volumes via the API
API Batch tutorial
API rate limit

API CLIENTS

Store credentials to access Seven Bridges client applications and libraries
R library
Client libraries
Python Library
Java library
Recipes
Java library Quickstart

SB Command Line Interface

Seven Bridges Command Line Interface
General commands
Billing
Projects and members
Files and metadata
Upload and download files
Apps
Tasks
Volumes

EDIT AN APP

About the editor
The tool editor
The workflow editor

ASYNC BULK ACTIONS

Overview
Copy multiple files
Delete multiple files and folders
Get details of a copy job
Get details of a deletion job
Get details of all async jobs
Move multiple files or folders
Get details of a move job

WES API

Overview
Run a workflow
Cancel a running workflow
Get the status of the workflow run
Get details of a workflow run
List workflow runs
Get service information

DATA STUDIO

About Data Studio
JupyterLab quick reference
RStudio quick reference
SAS Studio quick reference
Galaxy quick reference
OHIF Viewer quick reference
Run a Data Studio analysis
Data Studio analysis details
Copy a Data Studio analysis
Data Studio analysis charging
Data Studio environments and libraries
Data Studio analysis editor

SBFS (Beta)

About SBFS
Install SBFS manually
Install SBFS automatically
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
SBFS Log
Upgrade SBFS
Uninstall SBFS

SBFS Command Reference

Overview
Configure
List
Mount
Actions after mounting
Unmount
General commands

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