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Seven Bridges Command Line Interface Reference

GET STARTED

  • Before you start
  • Sign up for BioData Catalyst powered by Seven Bridges
  • Account settings
  • Manage dataset access
  • About the Payments page
    • Manage billing group members
  • Cloud infrastructure pricing
    • Compute costs
    • Storage costs
    • Data transfer costs

TUTORIALS

  • Getting started
  • Troubleshooting tutorial
  • Comprehensive user guide
  • Maintaining and versioning CWL on external tool repositories

GUIDES

  • Collaborating on the NHLBI BioData Catalyst(R): A Guide for Consortia
  • Estimate and Manage Your Cloud Costs
  • Using NHLBI BioData Catalyst® for Workshops and Courses
  • Create a multisample VCF from Variant Store
  • Share content through Public Projects
  • Guide to Billing Groups on BioData Catalyst

ACCESS THE PLATFORM

  • Sign up for BioData Catalyst powered by Seven Bridges
  • Switch from eRA Commons to login.gov
  • Access via the visual interface
  • Access via the API
  • Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

  • Projects on BioData Catalyst powered by Seven Bridges
  • Create a project
  • View a project
  • Manage the project dashboard
  • Modify project settings
  • Delete a project
  • Leave a project
  • Manage email notifications
  • Restrict file downloads

MANAGE FILES

  • Overview
  • File repositories on the Platform
  • Copy files using the visual interface
  • Copy files using the API
  • Search files on the Platform
  • Tag your files
  • Activity center
  • Archive files
    • Archive a file
    • Delete an archived file
    • Restore a file
  • Import individual files (Copy DRS URI)

BRING YOUR PRIVATE DATA

  • Upload your data to the Platform
  • 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 BioData Catalyst Powered by Gen3
  • Import from a DRS server
  • Import data from Gen3 BDC and Gen3 AnVIL

COLLABORATE SECURELY

  • Collaboration on BioData Catalyst powered by Seven Bridges
  • Add a collaborator to a project
  • Set permissions

BROWSE DATASETS

  • Study Variable Explorer

DATASETS HUB

  • TOPMed Data overview
  • ABOUT STUDIES
    • About data access
    • Framingham Cohort
    • NHLBI TOPMed: Genomic Activities such as Whole Genome Sequencing and Related Phenotypes in the Framingham Heart Study
    • Jackson Heart Study (JHS) Cohort
    • Multi-Ethnic Study of Atherosclerosis (MESA) Cohort
    • NHLBI TOPMed Jackson Heart Study
    • NHLBI TOPMed: MESA and MESA Family AA-CAC
    • Women's Health Initiative Clinical Trial and Observational Study
    • NHLBI TOPMed: Women's Health Initiative (WHI)
    • NHLBI TOPMed: Cleveland Clinic Atrial Fibrillation (CCAF) Study
    • Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older
    • NHLBI TOPMed: Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Project: Cardiovascular Health Study
    • Massachusetts General Hospital (MGH) Atrial Fibrillation Study
    • NHLBI TOPMed: Massachusetts General Hospital (MGH) Atrial Fibrillation Study
    • Heart and Vascular Health Study (HVH)
    • NHLBI TOPMed: Heart and Vascular Health Study (HVH)
    • Atherosclerosis Risk in Communities (ARIC) Cohort
    • NHLBI TOPMed: Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Project: ARIC
    • Genetic Epidemiology Network of Salt Sensitivity (GenSalt)
    • NHLBI TOPMed: Genetic Epidemiology Network of Salt Sensitivity (GenSalt)
    • GeneSTAR (Genetic Study of Atherosclerosis Risk) NextGen Consortium: Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
    • NHLBI TOPMed: GeneSTAR (Genetic Study of Atherosclerosis Risk)
    • Genetic Epidemiology Network of Arteriopathy (GENOA)
    • NHLBI TOPMed: Genetic Epidemiology Network of Arteriopathy
    • NHLBI TOPMed: San Antonio Family Heart Study
    • NHLBI TOPMed: Genetics of Cardiometabolic Health in the Amish
    • NHLBI TOPMed: Partners HealthCare Biobank
    • NHLBI TOPMed:The Vanderbilt Atrial Fibrillation Registry
    • NHLBI TOPmed: Novel Risk Factors for the Development of Atrial Fibrillation in Women
    • NHLBI TOPMed: The Vanderbilt AF Ablation Registry
    • NHLBI TOPMed: Diabetes Heart Study (DHS) African American Coronary Artery Calcification (AA CAC)
    • NHLBI TOPMed: HyperGEN - Genetics of Left Ventricular (LV) Hypertrophy
    • NHLBI TOPMed: Rare Variants for Hypertension in Taiwan Chinese (THRV)
    • NHLBI TOPMed: Genome-wide Association Study of Adiposity in Samoans
    • NHLBI TOPMed: Whole Genome Sequencing of Venous Thromboembolism (WGS of VTE)
    • NHLBI TOPMed - NHGRI CCDG: Hispanic Community Health Study/Study of Latinos
    • NHLBI TOPMed: Defining the time-dependent genetic and transcriptomic responses to cardiac injury among patients with arrhythmias
    • NHLBI TOPMed - NHGRI CCDG: The Johns Hopkins University School of Medicine Atrial Fibrillation Genetics Study
    • Coronary Artery Risk Development in Young Adults
    • NHLBI TOPMed - NHGRI CCDG: The BioMe Biobank at Mount Sinai
    • NHLBI TOPMed: Genetic Epidemiology of COPD
    • Genes-Environments and Admixture in Latino Asthmatics (GALA II) Study
    • NHLBI TOPMed - NHGRI CCDG: Genes-Environments and Admixture in Latino Asthmatics (GALA II)
    • NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados
    • NHLBI TOPMed: Boston Early-Onset COPD Study
    • NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)
    • NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica
    • NHLBI TOPMed: African American Sarcoidosis Genetics Resource
    • NHLBI TOPMed: Severe Asthma Research Program
    • NHLBI TOPMed: Childhood Asthma Management Program
    • NHLBI TOPMed: GOLDN Epigenetic Determinants of Lipid Response to Dietary Fat and Fenofibrate
    • NHLBI TOPMed: Recipient Epidemiology and Donor Evaluation Study-III Brazil Sickle Cell Disease Cohort
    • NHLBI TOPMed: Walk-PHaSST Sickle Cell Disease
    • NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe)
    • NHLBI TOPMed: The Cleveland Family Study (CFS)
    • NHLBI TOPMed: Pulmonary Hypertension and the Hypoxic Response in SCD
  • ABOUT METADATA FOR STUDIES
    • NHLBI studies metadata
  • QUERY DATASETS
  • About the Data Browser
    • Data Browser features
    • Data Browser query structure
    • Data Browser query: start by searching through a study
    • Data Browser query: start by searching for an ID
    • Data Browser query: start from an existing query
  • ACCESS DATA FROM DATASETS
    • Access data from the Data Browser
    • Data Browser features
    • Data model versions

PUBLIC GALLERY

  • Overview
  • Use public datasets
  • Use public files
  • Use public apps (workflows and tools)
  • Use Interactive Web Apps

PUBLIC PROJECTS

  • Human Cell Atlas Preview Datasets
  • Data Studio Interactive Analyses

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

USER GROUPS

  • Overview
  • Access your user group
  • Define homepage content
  • Define the policy
    • Edit your policy
    • Delete your policy
  • Manage group members
    • Invite a member to your group
    • Re-invite a member
    • Cancel the member invitation
    • Change the member's role
    • Remove a group member
    • Export information about group members
  • Leave a group

BRING YOUR TOOLS

  • About the SDK
  • About the Common Workflow Language
  • CWL v1.0 improvements over sbg:draft-2
  • CWL v1.2 conditional execution
  • About Docker
  • Install Docker
  • The BioData Catalyst Image Registry
  • Core Docker commands
  • Create and upload your Docker image
  • Create and upload your Docker image with a Dockerfile
  • Manage Docker repositories
  • Bring Nextflow apps to the Platform
  • Bring WDL apps to the Platform
  • Bring your Shiny apps to the BioData Catalyst
    • Developing Shiny applications for publishing
      • Local development
      • Development in the Data Studio and Custom Environments
    • 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

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
  • Run a task
  • Define app settings
  • About batch analyses
  • Project and file locations (Multi-cloud)
  • Import a Dockstore app
  • About secondary (index) files

TASK EXECUTION

  • About Spot/Preemptible Instances
  • Set execution hints at task level
  • Use Spot/Preemptible Instances
  • List of execution hints
  • List of available Amazon Web Services US East instances
  • List of available Google Cloud Platform instances
  • About Memoization (Reuse)
  • 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

INTERACTIVE ANALYSIS

  • Interactive analysis on the Platform
  • Seven Bridges Genome Browser
  • CummeRbundQC RNA-Seq Visualization
  • FastQC
  • Picard Alignment Summary metrics
  • The Seven Bridges Coverage app
  • TOPMed Annotation Explorer
  • Annotation Explorer

DOWNLOAD RESULTS

  • Download results

DEVELOPER TOOLS

  • Get your authentication token

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
  • Google Cloud Storage (GCS) Volumes
    • Attach a Google Cloud Storage volume
  • 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 Cloud storage tutorials
    • AWS Cloud storage tutorial
    • Google Cloud Storage tutorial

API Hub

  • API Overview
  • API Quickstart
  • Client libraries
  • Seven Bridges Command Line Interface
  • R library
  • Python Library
  • Java library
  • Java library Quickstart

API CLIENTS

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

DATA STUDIO

  • About Data Studio
  • JupyterLab quick reference
  • RStudio quick reference
  • SAS Studio 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

Seven Bridges Command Line Interface Reference

Suggest Edits

Overview

This section gathers the content of man pages (manual pages) for the commands in SB CLI. For brevity, global flags are listed only for the help command.

Conversely, learn how to access the Seven Bridges Command Line Interface.

Resources

  • General commands
  • Billing
  • Projects and members
  • Files and metadata
  • Upload and download files
  • Apps
  • Tasks
  • Volumes
  • Automations

Updated over 2 years ago


  • Table of Contents
    • Overview
    • Resources