Home Fundamentals Research Data Management FAIR Data Principles Metadata Ontologies Data Sharing Data Publications Data Management Plan Version Control & Git Public Data Repositories Persistent Identifiers Electronic Lab Notebooks (ELN) DataPLANT Implementations Annotated Research Context User Journey ARC specification ARC Commander QuickStart QuickStart (Experts) Swate QuickStart Walk-through Best Practices For Data Annotation DataHUB DataPLAN Ontology Service Landscape ARC Commander Manual Setup Git Installation ARC Commander Installation Windows MacOS Linux ARC Commander DataHUB Access Before we start Central Functions Initialize Clone Connect Synchronize Configure Branch ISA Metadata Functions ISA Metadata Investigation Study Assay Update Export ARCitect Manual Installation - Windows Installation - macOS Installation - Linux QuickStart ARCmanager Manual What is the ARCmanager? How to use the ARCmanager Swate Manual Swate Installation Excel Browser Excel Desktop Windows – installer Windows – manually macOS – manually Organization-wide Core Features Annotation tables Building blocks Building Block Types Adding a Building Block Using Units with Building Blocks Filling cells with ontology terms Advanced Term Search Templates File Picker Expert Features Contribute Templates ISA-JSON Workflows Manual CWL Introduction CWL runner installation CWL Examples CWL Metadata DataHUB Manual Overview User Settings Generate a Personal Access Token (PAT) Projects Panel ARC Panel Forks Working with files ARC Settings ARC Wiki Groups Panel Create a new user group Data publications Passing Continuous Quality Control Submitting ARCs with ARChigator Track publication status Use your DOIs Guides ARC User Journey Create your ARC ARC Commander QuickStart ARC Commander QuickStart (Experts) ARCitect QuickStart Annotate Data in your ARC Annotation Principles ISA File Types Best Practices For Data Annotation Swate QuickStart Swate Walk-through Share your ARC Register at the DataHUB DataPLANT account Invite collaborators to your ARC Work with your ARC Using ARCs with Galaxy Recommended ARC practices Syncing recommendation Keep files from syncing to the DataHUB Working with large data files Adding external data to the ARC ARCs in Enabling Platforms Publication to ARC Contribute Swate Templates Knowledge Base Teaching Materials Slides DataPLANT Annotated Research Context Videos Start Your ARC Series Events 2023 Nov: CEPLAS PhD Module Oct: CSCS CEPLAS Start Your ARC Sept: MibiNet CEPLAS Start Your ARC July: RPTU Summer School on RDM July: Data Steward Circle May: CEPLAS Start Your ARC Series Frequently Asked Questions

Using ARCs with Galaxy

last updated at 2024-01-23 About this guide

In this guide we introduce how to access ARCs from Galaxy. To access the data of an ARC, you must first provide a DataHUB access token in Galaxy, which is used to authenticate Galaxy to DataHUB. To create a new token and add it to Galaxy, you can proceed as described below.

UserAdvanced ModeTutorial

Before we can start

☑️ You have created an ARC before using the ARC Commander or ARCitect
☑️ You have a DataPLANT account

Create an access token in DataHUB

image image

  1. Open the dropdown menu for your personal settings.
  2. Open the "Preferences" menu.
  3. Change to tab "Access Tokens".
  4. Choose a name for the new token.
  5. Set a expiration date.
  6. Select the authorization scope.

💡 Only the scopes "api" (for write access) and "read_api" (for read access) are relevant for ARCfs.
Important: After you crated the token, you can copy and view it. After you leave the site, you will not be able to do so again.

Add the token to Galaxy

image image image image

  1. Visit usegalaxy.eu and log in or create an account. It is possible to log in using your DataPlant account.
  2. Open the "User" drop down menu and
  3. select "Preferences".
  4. In the user preference settings, select "Manage Information".
  5. Copy your token into the "API read access token" field. This filed is located at the bottom of the "User preferences" menu. Click "Save" to adopt your changes.

💡 Despite the name "API read access token", tokens with write access rights (like those with the scope "api") will also work or, respectively, are required.

Data import

With the token available to Galaxy, you are now able to import data. You can do this as described below.

image image image image

  1. Click on the "Upload Data".
  2. Pick "Choose remote files".
  3. Scroll down and select "DataPLANT DataHub ARRCs".
  4. Explore ARCs or
  5. search for a specific one.
  6. Inside an ARC, choose the file you want to import to Galaxy. Confirm with "Ok".
  7. Click start to begin the import process to Galaxy. This may take some time, depending on the workload on the Galaxy server and the size of your file.
Data export

It is also possible to export datasets back to an ARC. You can do this as described below.

image image image

  1. On the left sidebar, open the menu "Send Data".
  2. Select "Export datasets" to remote files source.
  3. In the opening menu, select "DataPLANT DataHUB ARCs".
  4. Select or
  5. search for an ARC.
  6. Chose a directory inside an ARC where your dataset should be stored.
  7. Choose the dataset you want to export,
  8. Clock on "Run Tool" to start the export process. This may take some time, depending on the workload on the Galaxy server and the size of your file.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
Contribution Guide 📖
✏️ Edit this page