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Using ARCs with Galaxy

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.

Create an access token in DataHUB

Section titled Create an access token in DataHUB

This guide shows you how to generate a Personal Access Token (PAT). The PAT can be used to authenticate your local machine to communicate with your DataHUB account.

  1. Sign in to the DataHUB

  2. Navigate to the user settings

  3. Go to the Access Tokens settings

  4. Fill all required information:

    • Token name: e.g. the name of the machine to be linked (“Office PC”) (1)
    • Expiration date (optional) (2)
    • Select a scope: e.g. api (3)
  5. Click “Create personal access token” (4)

  6. Your new personal access token appears on top. Copy (1) it somewhere safe for later use.

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  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.

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

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  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.

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

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  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.

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