Code Ocean User Guide
v3.6.0
v3.6.0
  • Welcome to Code Ocean
  • Onboarding
    • Quick Start Guides
      • Create a Capsule in 5 minutes
      • Create a Pipeline in 5 minutes
    • Video Library
  • Key Concepts
  • Capsule Guide
    • The Capsule Interface
      • File Navigation/App Builder Panel
      • Editor Panel
      • Reproducibility Panel
    • The Structure of a Capsule
      • Metadata
      • Environment
      • Code
      • Data
      • .codeocean
      • Scratch
      • Results
    • Reproducible Runs
    • Version Control
      • Importing a Capsule from a Git Provider
      • Clone via Git...
    • Managing Capsules
      • Sharing a Capsule with Secrets
      • Exporting Capsules to your Local Machine
    • Secret Management Guide
      • Setting a Secret in the Account Settings Page
      • Accessing a Secret in a Capsule
  • Setting up the Environment
    • Selecting a Starter Environment
    • Package Managers and Adding Packages
    • Installing R packages
    • Environment Variables
    • Build Log
    • Post-Install Script
    • Compute Resources
  • Working in a Cloud Workstation
    • Launching a Cloud Workstation
      • Running RShiny in Code Ocean
      • Running Streamlit in Code Ocean
      • Using Terminal in Code Ocean
      • Using Ubuntu Desktop in Code Ocean
      • Using MATLAB in Code Ocean
      • Using VS Code in Code Ocean
    • Exiting a Cloud Workstation Session
  • Data Assets Guide
    • Types of Data Assets
    • Creating a New Data Asset
    • Capturing a Result
      • Provenance of the Result Data Asset
    • Using Data Assets in a Capsule
    • Managing Data Assets
      • Finding Data Assets
        • Custom Metadata
  • Pipeline Guide
    • The Pipeline UI
      • File Tree System
      • Pipeline App Panel
      • Timeline
    • Components of a Pipeline
      • Nextflow File
      • Capsules
      • Data
      • Results Bucket
      • Map Paths
      • Capsule Settings
      • Pipeline Settings
      • .codeocean
    • Managing Pipelines
      • Exporting Pipelines to your Local Machine
    • Capsule vs Pipeline Differences
    • How to Run Code in Parallel
    • Nextflow Configurations
    • Pipeline Monitoring
      • Monitoring Dashboard
      • Task Details
    • Nextflow Artifacts
    • nf-core Pipelines
      • Import nf-core pipelines
      • nf-core RNASeq Tutorial
        • iGenomes
    • Pipeline Tutorial
  • Release Capsules and Pipelines
    • Creating and Using Release Capsules
    • Creating Release Pipelines
    • Internal Releases
  • Collections
  • Code Ocean Apps
    • Genomics
    • Cheminformatics
    • Visualization
    • Machine Learning
    • Data Connectors
    • Quality Control
    • Use Cases and Examples
      • CombFold Pipeline
      • Data Connector Example
      • Gene Set Enrichment Overview
      • RNASeq Quantification Pipeline
  • App Panel Guide
    • App Builder User Interface
      • Validation pattern for strings
    • Passing App Panel's Parameters to the Script
    • Releasing an App Panel Capsule
    • Executing an App Panel Capsule
  • MLflow Guide
    • Enable MLflow Tracking
    • MLflow UI
    • Creating Models
    • MLflow Permissions
  • Models Guide
    • Creating Models
    • Managing Models
  • Git Provider Integration Guide
    • Setting up the Integration
    • Using Git Provider Integration
  • Code Ocean API
    • Authentication
    • Errors
    • Capsule
    • Computation
    • Data Asset
    • Python SDK
  • More Support
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On this page
  • Attaching Data Assets to a Capsule
  • From the IDE
  • From a Cloud Workstation (e.g., RStudio, Terminal, or Jupyter)
  • Viewing the Detail of the Data Asset when attaching
  • Renaming the Mounting Point (Folder)

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  1. Data Assets Guide

Using Data Assets in a Capsule

PreviousProvenance of the Result Data AssetNextManaging Data Assets

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Attaching Data Assets to a Capsule

A single Data Asset can simultaneously be used by multiple users across many Capsules or Pipelines. This is possible because Data Assets are independent cloud storage.

From the IDE

  1. Go to the data folder and click Manage Data Assets.

  2. Attach/Detach Data side panel will appear. Click on the plus sign to attach the Data Asset.

If a Data Asset has been set as default in the App Builder, replace the Data Asset from the App Panel by clicking the replace button.

From a Cloud Workstation (e.g., RStudio, Terminal, or Jupyter)

  1. Click Manage Data in the header of the Cloud Workstation.

  2. Attach/Detach Data side panel will appear. Click on the plus sign to attach the Data Asset.

When attaching an external Data Asset, the following points should be considered:

  1. To link to an external Data Asset, you need to have an appropriate secret or Assumed Role in your Code Ocean account which grants access to the AWS S3 location. Code Ocean will automatically use the appropriate credentials to access the data without needing to explicitly add the secret or Assumed role to the Capsule environment.

  2. Due to AWS S3 behavior, it takes time to reach files.

Viewing the Detail of the Data Asset when attaching

From the Attach/Detach Data page, metadata can be viewed without leaving the Cloud Workstation page.

To retrieve this information:

  1. Hover over the data asset, which does not have to be attached

  2. Click Data Details

While in the Cloud Workstation, the same Data information will display as on the Data dashboard.

After the Data Asset has been attached to the Capsule or Pipeline, you can find the Data details in the drop-down menu.

Renaming the Mounting Point (Folder)

After you have attached a Data Asset to your Capsule, you can change the name of the mounting point (that is, the folder name) in the Code Ocean IDE.

  1. Hover over the attached dataset under the /data folder.

  2. Click on the down arrow.

  3. Select Rename.