Get started

• Before you start
• Sign up for CAVATICA
• New for CAVATICA
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Tutorials

• Build a workflow tutorial
• Upload a custom Python program using a Dockerfile
• Create a tar archive
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Access CAVATICA

• Access via the visual interface
• Access via the API
• Set up two-factor authentication

CAVATICA Projects

• Projects overview
• Manage the project dashboard
• Controlled projects
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MANAGE FILES

• Overview
• File repositories on CAVATICA
• Copy files using the visual interface
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Bring data to CAVATICA

• Upload your data to CAVATICA
• Upload from your computer
• Upload via the command line
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Find apps

• Apps on CAVATICA
• Workflows and tools
• Interactive Web Apps

Set metadata associated with a file

• Metadata on CAVATICA
• System metadata
• Metadata schema
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Collaborate securely

• Collaboration on CAVATICA
• Add a collaborator to a project
• Set permissions

Bring your tools

• About the SDK
• About the Common Workflow Language
• CWL v1.0 improvements over sbg:draft-2
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Docker

• About Docker
• Install Docker
• The image registry
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Developer tools

• Get your authentication token
• Publish your app in the Public Apps gallery

Edit an app

• About the editor
• About the tool editor
• Introduction to tool wrapping
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Tool wrapping tips and tricks

• Javascript Cookbook
• Set suggested input values for CWL v1.x apps

Describe your tool (Legacy)

• The tool editor
• Create a workflow
• Edit a workflow
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Public projects

• Bulk RNA-Seq Transcription Profiling of HSV-1 Infected Cells
• Meta-Analysis Of Cytometry Data From ImmPort Data Repository
• INCLUDE Linear Regression Tutorial: step-by-step instructions
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Guides

• Secure Configuration Guide

Browse public datasets

• Introduction to datasets
• TCGA data
• TCGA data access
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Run an analysis

• About analyses
• About batch analyses
• Run a task
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SB COMMAND LINE INTERFACE

• Seven Bridges Command Line Interface
• Seven Bridges Command Line Interface Reference

Task Execution

• About task execution
• About Spot/Preemptible Instances
• Use Spot/Preemptible Instances
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Review a task

• Review the task page
• View task stats
• View task logs
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Interactive Browsers

• Genome Browser

Kids First studies

• Kids First studies overview and access

CAVATICA Datasets

• CAVATICA datasets overview
• Access to CAVATICA datasets

Connect cloud storage

• Volumes
• Aliases
• Amazon Web Services Simple Storage Service (S3) volumes
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SBFS (Beta)

• About SBFS
• Install SBFS automatically
• Install SBFS manually
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Data Studio

• About Data Studio
• JupyterLab quick reference
• RStudio quick reference
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Analysis results

• Download results
• View output files

SBFS Command reference

• Overview
• Configure
• List
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FHIR Viewer

• Getting started
• Connect to a FHIR server
• Viewer interface reference
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