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GET STARTED

  • About the Seven Bridges Platform
    • Time synchronization
  • Before you start
  • QuickStart
  • Account settings
  • About the Payments page
  • Manage your subscription
  • Cloud infrastructure pricing
    • Compute costs
    • Storage costs
    • Data transfer costs
  • Developer Dashboard
  • Email notifications page

TUTORIALS

  • Seven Bridges Platform tutorials
  • Build a workflow tutorial
  • Worked example of uploading SAMtools Sort
  • Upload a custom Python program using a Dockerfile
  • Create a tar archive
  • Troubleshooting tutorial
  • Comprehensive tips for reliable and efficient analysis set-up

ACCESS THE SEVEN BRIDGES PLATFORM

  • Sign up for the Seven Bridges Platform
  • Access via the visual interface
  • Access via the API
  • Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

  • Projects on the Seven Bridges Platform
  • Create a project
  • View a project
  • Manage the project dashboard
  • Modify project settings
  • Set file download restriction
  • Manage email notifications
  • Add notes to your project
  • Leave a project
  • Delete a project
  • Tag your projects

COLLABORATE SECURELY

  • Collaboration on the Seven Bridges Platform
  • Add a collaborator to a project
  • Set permissions

DATASETS HUB

  • About datasets

BRING YOUR PRIVATE DATA

  • Upload your data to the Seven Bridges Platform
  • Upload from your computer
  • Upload via the command line
  • Import from an FTP/HTTP(S) server
  • Upload via the API
  • Import from a Volume
  • Import from a DRS server

SET METADATA ASSOCIATED WITH A FILE

  • Metadata on the Seven Bridges Platform
    • 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

SEARCH FILES

  • File repositories on the Seven Bridges Platform
  • Search files on the Platform

ADD FILES TO A PROJECT

  • Add files using the visual interface
  • Copy files using the API
  • Tag your files

ORGANIZE FILES

  • Available actions
  • Activity center

ARCHIVE FILES (on AWS)

  • File archiving overview
  • Archive a file
  • Restore a file
  • Delete an archived file

ARCHIVE APPS

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

SBFS (Beta)

  • About SBFS
  • Install SBFS automatically
  • Install SBFS manually
  • Configure SBFS credentials
  • List available projects for SBFS
  • Mount a project
  • Unmount a project
  • Command reference
    • Configure
    • List
    • Mount
    • Actions after mounting
    • Unmount
    • General commands
  • SBFS Log
  • Upgrade SBFS
  • Uninstall SBFS

FIND APPS

  • Apps on the Seven Bridges Platform
    • Publish a third-party app or workflow
  • Search for an app
  • Explore app details
  • App versions
  • Interactive Web Apps

BRING YOUR TOOLS

  • About the SDK
  • About the Common Workflow Language
  • CWL v.1.0 improvements over sbg:draft-2
  • CWL v1.2 conditional execution
  • Bring Nextflow apps to the Platform
    • Add Nextflow apps through the command line interface (CLI)
    • Add Nextflow apps through the visual interface
    • Manage Nextflow apps on the Platform
    • Set execution mode for Nextflow apps
    • sbpack_nf command reference
    • Nextflow Quickstart Tutorial
    • Nexttflow CLI app upload tutorial
    • Using Sample Sheets with Nextflow Apps on the SevenBridges Platform
  • Bring WDL apps to the Platform

DOCKER

  • About Docker
  • Install Docker
    • Install Docker on Linux
    • Install Docker on macOS
    • Install Docker on Windows
  • Image registries
    • About the Seven Bridges Image Registry
    • About Docker Hub
  • Create and upload a Docker image
  • Create and upload a Docker image with a Dockerfile
  • Manage Docker repositories
  • Core Docker commands
  • Docker for Enterprise
  • Mount a USB drive in a Docker container
  • Docker best practice recommendations

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
  • Forking tools

TOOL WRAPPING TIPS AND TRICKS

  • 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

COPY AN APP

  • Copy public apps to a project
  • Copy an app from a project

EDIT AN APP (LEGACY)

  • Edit a tool
  • Create a workflow
  • Edit a workflow
  • Add revision notes

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

RUN AN ANALYSIS

  • About analyses
  • About batch analyses
  • Run a task
  • Define app settings
  • Set computation instances
  • About secondary (index) files

TASK EXECUTION

  • About task execution
  • About controlling task execution
  • About parallelizing tool executions (Scatter)
  • 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 Instances
  • Use Spot Instances
  • List of execution hints
  • List of task statuses
  • List of available Amazon Web Services US instances
  • List of available Amazon Web Services EU instances

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 Platform
  • Seven Bridges Genome Browser
  • Variant Browser
  • VCF Benchmarking app
  • CummeRbundQC RNA-Seq Visualization
  • FastQC
  • Picard Collect Alignment Summary Metrics
  • The Seven Bridges Coverage app

RHEO

  • Overview
  • Manage via CLI
  • Manage via API
  • Manage via RHEO visual interface (GUI)
  • RHEO glossary

RHEO FOR DEVELOPERS

  • Overview
  • RHEO Developer tutorial
    • Installation and configuration
    • Hello world!
    • Step inputs
    • Step nesting, promises, and dependencies
    • Parallelization and promises
    • Loops and result gathering
    • Conditionals
    • Automating the Seven Bridges Platform
    • Config files and automation settings
    • App-executing steps
    • Singletons and contexts
    • Type checking
    • Deploy and run automations on the Seven Bridges Platform
    • Using the RHEO visual interface (GUI)
    • Repository structure
  • Create automations for the RHEO visual interface (GUI)
    • Automation inputs
    • Automation outputs

GRAPH GENOME APPS

  • About Graph Genome apps
  • Graph WGS
    • About Graph WGS
    • Graph Germline Variant Detection Workflow tutorial

DATA STUDIO

  • About Data Studio
  • JupyterLab quick reference
  • RStudio quick reference
  • Run a Data Studio analysis
  • Data Studio analysis details
  • Copy a Data Studio analysis
  • Data Studio analysis charging
  • Data Studio analysis editor
  • Data Studio environments and libraries

DOWNLOAD RESULTS

  • Download results

DEVELOPER TOOLS

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

PUBLIC PROJECTS

  • Public projects overview
  • Smart Variant Filtering
  • Data Studio Interactive Analyses
  • VCF Benchmarking
  • Cancer Cell Line Encyclopedia (CCLE)
  • Simons Genome Diversity Project (SGDP) dataset
  • Human Cell Atlas Preview Datasets

ENTERPRISE FEATURES

  • About the Enterprise feature
  • Collaboration within an Enterprise
  • Manage an Enterprise
    • Create a Division
    • Manage Division administrators
    • Review billing information for all Divisions
    • Review Enterprise data throughput
  • Manage a Division
    • Manage Division members
    • Manage teams
    • Review billing information for your Division
    • Set credit card as payment method
    • Manage Division notifications
  • Add a collaborator to an Enterprise project
  • Switch between Divisions
  • Manage two-factor authentication
  • Manage Docker repositories
  • Single sign-on (SSO) setup

API Hub

  • API Overview
  • API tutorials
    • Introduction to the API tutorial
    • API Quickstart
    • API Batch tutorial
  • API rate limit
    • Submitting tasks for execution
    • Copying files between projects
    • Importing files from a volume
    • Updating file metadata
    • Deleting multiple files
    • Exporting files to a volume
    • Setting maximum pagination limit in queries
    • Finding project by name
  • Using volumes via the API

API CLIENTS

  • API Clients
  • Store credentials to access Seven Bridges client applications and libraries
  • R library
  • Python library recipes
  • Python library
  • Java library
  • Java library Quickstart
  • Seven Bridges Command Line Interface
  • Seven Bridges Command Line Interface Reference
    • General commands
    • Billing
    • Projects and members
    • Files and metadata
    • Upload and download files
    • Apps
    • Tasks
    • Volumes

Connect cloud storage

  • Connect cloud storage overview
  • Volumes
  • Aliases
  • Supported cloud storage providers
  • Amazon Web Services Simple Storage Service (AWS S3) Volumes
  • Google Cloud Storage (GCS) Volumes
  • Security concerns when working with volumes
  • Enabling cross-origin resource sharing (CORS)
  • Operations on volumes
    • About volumes on the visual interface
    • Attach an Amazon Web Services (AWS) volume
    • Attach a Google Cloud Storage volume
    • Manage members for a volume
    • Browse and add files to a project from a volume
    • Deactivate a volume
  • API Cloud storage tutorials
    • AWS Cloud storage tutorial
    • Google Cloud Storage tutorial

GLOSSARY

  • Glossary

Image registries

Suggest Edits

An image registry stores Docker images. Each registry is organized into collections of images, called repositories.

Available registries include the Seven Bridges Image Registry and Docker Hub, Docker’s own image registry.

Updated over 6 years ago