Using Galaxy in combination with NRP repositories

This page describes how to use usegalaxy.cz with repositories of the National Repository Platform (official NRP page).

Using the NRP catch-all repositoryCopy Anchor Link

The following steps describe how to obtain data from the NRP catch-all repository, run a workflow, and export the results back. The catch-all repository is available at https://datarepo.eosc.cz/.

Step 1: Obtain an access token from the repositoryCopy Anchor Link

1. Navigate to the NRP catch-all repository at https://datarepo.eosc.cz/.
2. Log in with your e-INFRA CZ AAI credentials.
3. Navigate to your profile settings, find the Applications section, and choose the option to generate a new personal access token.
4. Create a new token with the user:email scope.
5. Copy the generated token to your clipboard. Treat this token like a password and keep it secure.

Step 2: Store the token in GalaxyCopy Anchor Link

1. Log in to your usegalaxy.cz account.
2. Click on your username in the top menu and select Preferences.
3. In the user preferences menu, find and click on Manage Information.
4. Find an entry labeled Your CESNET-Invenio datarepo Account and paste your token into the value field.
5. Save the changes. Galaxy stores the token and uses it to access the repository.

Step 3: Import data from the repositoryCopy Anchor Link

1. In the Galaxy interface, go to the Upload Data tool in the left-hand tool panel.
2. From the upload options, select Choose remote files.
3. From the available options select CESNET-Invenio datarepo.
4. Search for data in the repository at datarepo.eosc.cz.
5. Select the desired files and click Import to bring them into your Galaxy history.

Step 4: Run a workflowCopy Anchor Link

Run a workflow on the imported data. You can create a new workflow or import an existing one. For a general guide on using workflows in Galaxy, see the official documentation.

Step 5: Export the workflow invocation to the repositoryCopy Anchor Link

Once the workflow has finished running, you can export the entire workflow invocation, including the results and provenance information. Galaxy exports it in the RO-Crate format, a standard for packaging research objects.

1. Go to User → Workflow Invocations at the top of the Galaxy interface to see a list of your workflow runs. Select the one you want to export.
2. On the workflow invocation page, click the Export button.
3. In the export wizard, configure the following options:
   • As the format select Workflow Run RO-Crate.
   • For the destination select RDM repository.
   • For creating the record select repository CESNET-Invenio datarepo.
   • Name the record and create it.
   • Finally, export the workflow invocation to the newly created record.
4. The workflow invocation is packaged as an RO-Crate and deposited into the repository. This makes your analysis easier to reproduce and documents how the results were produced.

For details on how Galaxy dataset metadata maps to the metadata model used by NRP repositories, see Galaxy dataset ↔ CCMM mapping.