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Guides

The Case Explorer

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

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
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 METADATA FOR STUDIES
- NHLBI studies metadata
QUERY DATASETS
About the Data Browser
ACCESS DATA FROM DATASETS

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
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

EDIT AN APP

About the editor
The tool editor
The workflow editor

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

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

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