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Seven Bridges knowledge center Documentation

Home Guides API Reference Release notes

v1.0

Seven Bridges knowledge center Documentation

Guides

v1.0Home Guides API Reference Release notes

Get started

Before you start
Sign up for CAVATICA
New for CAVATICA
CAVATICA quickstart
Account Settings
Payments page
Manage billing groups
Email notifications page
Cloud Credits on CAVATICA
Connect to a DRS server
Access TCGA data from CAVATICA
Upgrade your account (ERA Commons)
Set up two-factor authentication
Cloud infrastructure pricing
Developer dashboard

Tutorials

Build a workflow tutorial
Upload a custom Python program using a Dockerfile
Create a tar archive
Bring Your Own Tool(s) to CAVATICA
Maintaining and versioning CWL on external tool repositories
Estimate and Manage Your Cloud Costs
Collaborating on CAVATICA: A Guide for Consortia
Seamless access to the Sequence Read Archive (SRA) data on Cavatica

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
Create a project
View a project
Modify project settings
Restrict file downloads
Manage email notifications
Add notes to your project
Leave a project
Delete a project

MANAGE FILES

Overview
File repositories on CAVATICA
Copy files using the visual interface
Copy files using the API
Search files on CAVATICA
Tag your files
Activity center
Archive files (AWS)
Import individual files (Copy DRS URI)
New File Browser

Bring data to CAVATICA

Upload your data to CAVATICA
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 from a DRS server
Import from ELITE portal
Import data from ICDC
Import from the PDC
Import data from CDS
Import data from Gen3 BDC and Gen3 AnVIL
Import data from Gen3 AnVIL to CAVATICA Cloud
Dynamic PFB Importer

Find apps

Apps on CAVATICA
Workflows and tools
Interactive Web Apps

Set metadata associated with a file

Metadata on CAVATICA
System metadata
Metadata schema
Edit metadata using the visual interface
Edit metadata with a manifest
Edit metadata using the command line uploader
Export metadata to a manifest
Edit metadata using the API
Metadata manifest file format
Generate DRS manifest

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
CWL v1.2 conditional execution
Bring Nextflow apps to CAVATICA
Bring WDL apps to CAVATICA

Docker

About Docker
Install Docker
The image registry
Create and upload your Docker image
Create and upload your Docker image with a Dockerfile
Core Docker commands
Manage Docker repositories
Mount a USB drive in a Docker container

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
Create a tool
Tool editor tutorial
Input file options
Advanced practices
Dynamic expressions in tool descriptions
Javascript Cookbook
About the workflow editor
Create a workflow
Workflow editor tutorial
About the workflow editor

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
Dynamic expressions in tool descriptions

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
INCLUDE HTP DESeq2 Tutorial: Step-by-step instructions

Browse public datasets

Introduction to datasets
TCGA data
TCGA data access
TCGA GRCh38 data
CCLE data
TARGET GRCh38 data
CPTAC data
CCLE metadata
TCGA GRCh38 metadata
TARGET GRCh38 metadata
CPTAC metadata
CPTAC-3 metadata
The Data Browser
Data Browser features
Data model versions
Data Browser query structure
Data Browser query: start from an example
Data Browser query: start by searching through a dataset
Data Browser query: start from an existing query
Data Browser query: start from scratch
Data Browser query: multiple dataset query
Access data from the Data Browser

Run an analysis

About analyses
About batch analyses
Run a task
About Memoization (Reuse)
Project and file locations (Multi-cloud)
Import Dockstore apps to Cavatica
Define app settings
About secondary (index) files

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
Set computation instances
List of available Amazon Web Services US East instances
List of available Google Cloud Platform instances
List of execution hints
Set execution hints at node level
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 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
Attach an Amazon Web Services S3 volume
Attach a Google Cloud Storage volume
Attach a volume through an S3-compatible endpoint
Enabling cross-origin resource sharing (CORS)
Connect cloud storage overview

SBFS (Beta)

About SBFS
Install SBFS automatically
Install SBFS manually
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
SBFS Log
Upgrade SBFS
Uninstall SBFS
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

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 environments and libraries
Data Studio analysis editor
Public Interactive Analyses

Analysis results

Download results
View output files

SBFS Command reference

Overview
Configure
List
Mount
Unmount
General commands

FHIR Viewer

Getting started
Connect to a FHIR server
Viewer interface reference
Write and run queries
Understand results
Export to Project
Case study: Cohort-to-files workflow
Troubleshooting and support

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Edit a workflow