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v1.0

Seven Bridges knowledge centerDocumentationCAVATICA
v1.0HomeGuidesAPI ReferenceRelease notes

Get started

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

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
  • Manage email notifications
  • Add notes to your project
  • Leave a project
  • Delete a project

Find apps

  • Apps on CAVATICA
  • Workflows and tools
    • Search for an app
    • Explore app details
    • App versions
    • Copy public apps to a project
  • Interactive Web Apps

Organize files

  • Search files on CAVATICA
  • Copy files using the visual interface

Archive files (AWS)

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

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 data from ICDC
  • Import from the PDC
  • Import data from Gen3 BDC and Gen3 AnVIL

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
    • MetaCyto Analysis Instructions
    • Project description
    • MetaCyto Analysis Walkthrough
    • MetaCyto Homework assignment

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 (WorkReuse)
  • Project and file locations (Multi-cloud)
  • Import Dockstore apps to Cavatica
  • Define app settings
  • About secondary (index) files

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

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

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

Analysis results

  • Download results
  • View output files

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
  • Unmount
  • General commands

Meta-Analysis Of Cytometry Data From ImmPort Data Repository

Suggest Edits
  • MetaCyto Analysis instructions
  • MetaCyto project description
  • MetaCyto analysis walkthrough
  • MetaCyto homework assignment

Updated 25 days ago