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v1.0

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v1.0HomeGuidesAPI 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
    • Archive a file
    • Restore a file
    • Delete an archived file
  • Import individual files (Copy DRS URI)

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

COLLABORATE SECURELY

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

DATASETS HUB

  • ABOUT DATASETS
  • About data access
  • TCGA data
  • TCGA GRCh38 data
  • CCLE data
  • Foundation Medicine data
  • SGDP data
  • TCIA data
  • CPTAC data
  • TARGET GRCh38 data
  • ICGC data
  • PGP-UK data
  • ABOUT METADATA FOR DATASETS
  • TCGA metadata
  • TCGA GRCh38 metadata
  • CCLE metadata
  • CPTAC metadata
  • CPTAC-3 metadata
  • TCIA Metadata
  • TARGET GRCh38 metadata
  • ICGC metadata
  • PGP-UK metadata
  • BROWSE DATASETS
  • About the Data Overview
  • ↳ Data Overview features
  • ↳ Use the Data Overview
  • About the Case Explorer
  • ↳ Case Explorer features
  • ↳ Use the Case Explorer
  • QUERY DATASETS
  • About the Data Browser
  • ↳ Data Browser features
  • ↳ Data model versions
  • ↳ Data Browser query structure
  • ↳ Data Browser query: start from an example query
  • ↳ Data Browser query: start by searching through a dataset
  • ↳ Data Browser query: start from scratch
  • ↳ Data Browser query: start from an existing query
  • ↳ Data Browser query: multiple dataset query
  • ↳ Data Browser query: start by searching for an ID
  • About the Datasets API
  • ↳ Browse datasets via the Datasets API
  • ↳ Query via the Datasets API
  • ↳Search via the Datasets API
  • ACCESS DATA FROM DATASETS
  • Access data from the Data Browser
  • Access data from the Datasets API
  • Dataset ontologies
  • Manifest files for datasets

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
    • Search for an app (workflow or tool)
    • Explore app details
    • App versions
  • 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
    • Developing Shiny applications for publishing
      • Local development
    • App registration
    • sbShinyModules Package Usage Guidelines
      • Installation
      • Key modules
      • File picker module
      • Plot exporter module
      • Generic file exporter module
      • Additional features available in the package

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
    • About the tool editor
    • Introduction to tool wrapping
    • Create a tool
    • Tool editor tutorial
    • Input file options
    • Advanced practices
    • Dynamic expressions in tool descriptions
    • Javascript Cookbook
  • The workflow editor
    • About the workflow editor
    • Create a workflow
    • Workflow editor tutorial

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

Folders Overview

Suggest Edits

The feature allows you to create and organize folders on the CGC via dedicated API calls. Folders are created inside projects, and can be used to contain files within the project.

Creating folders on the CGC allows you to mirror an external file structure with your files inside a project.

The following API calls have been added:

  • Create a folder
  • List folder contents
  • Move a file between folders
  • Copy a file between folders
  • Delete a folder

Updated over 2 years ago