This page describes a work-in-progress integration of usegalaxy.cz with repositories of the National Repository Platform (official NRP page).

Using the CESNET Invenio CatchAll repository

The following steps will guide you through the process of obtaining data from a CESNET Invenio repository, running a workflow, and exporting the results back. The repository used in this example is available at https://workflow-repo.test.du.cesnet.cz/.

Step 1: Obtain an Access Token from the Repository

1. Navigate to the CESNET Invenio repository at https://workflow-repo.test.du.cesnet.cz/.
2. Log in with your E-infra 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 Galaxy

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 CatchAll Account and paste your token into the value field.
5. Save the changes. This will securely store your token within Galaxy for later use.

Step 3: Import Data from the Repository

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 TESTING.
4. You will be presented with the search functionality to find data within the repository at workflow-repo.test.du.cesnet.cz.
5. Select the desired files and click Import to bring them into your Galaxy history.

Step 4: Run a Workflow

1. With the data in your history, you can now run an analysis.
2. You can create a new workflow or import an existing one. For a general guide on using workflows in Galaxy, see the official documentation.
3. Run the workflow on your imported data.

Step 5: Export Workflow Invocation to the Repository

1. Once the workflow has finished running, you can export the entire workflow invocation, including the results and provenance information.
2. 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.
3. Galaxy supports exporting this information in the RO-Crate format, which is a standard for packaging research objects.
4. From the workflow invocation page, click the Export button.
5. 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 TESTING.
   • Name the record and create it.
   • Finally, export the workflow invocation to the newly created record.
6. The workflow invocation will be packaged as an RO-Crate and deposited into the repository. This ensures that your analysis is reproducible and well-documented.