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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