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| 1 | +--- |
| 2 | +title: Using Galaxy in combination with NRP repositories |
| 3 | +--- |
| 4 | + |
| 5 | +This page describes a work-in-progress integration of [usegalaxy.cz](https://usegalaxy.cz) with repositories of the National Repository Platform ([official NRP page](https://www.eosc.cz/en/projects/national-repository-platform-for-research-data-nrp/national-repository-platform)). |
| 6 | + |
| 7 | +# Using the CESNET Invenio CatchAll repository |
| 8 | + |
| 9 | +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/](https://workflow-repo.test.du.cesnet.cz/). |
| 10 | + |
| 11 | +## Step 1: Obtain an Access Token from the Repository |
| 12 | + |
| 13 | +1. Navigate to the CESNET Invenio repository at [https://workflow-repo.test.du.cesnet.cz/](https://workflow-repo.test.du.cesnet.cz/). |
| 14 | +2. Log in with your E-infra AAI credentials. |
| 15 | +3. Navigate to your profile settings, find the **Applications** section, and choose the option to generate a new personal access token. |
| 16 | +4. Create a new token with the `user:email` scope. |
| 17 | +5. Copy the generated token to your clipboard. **Treat this token like a password and keep it secure.** |
| 18 | + |
| 19 | +## Step 2: Store the Token in Galaxy |
| 20 | + |
| 21 | +1. Log in to your [usegalaxy.cz](https://usegalaxy.cz) account. |
| 22 | +2. Click on your username in the top menu and select **Preferences**. |
| 23 | +3. In the user preferences menu, find and click on **Manage Information**. |
| 24 | +4. Find an entry labeled **Your CESNET-Invenio CatchAll Account** and paste your token into the value field. |
| 25 | +5. Save the changes. This will securely store your token within Galaxy for later use. |
| 26 | + |
| 27 | +## Step 3: Import Data from the Repository |
| 28 | + |
| 29 | +1. In the Galaxy interface, go to the **Upload Data** tool in the left-hand tool panel. |
| 30 | +2. From the upload options, select **Choose remote files**. |
| 31 | +3. From the available options select **CESNET-Invenio TESTING**. |
| 32 | +4. You will be presented with the search functionality to find data within the repository at `workflow-repo.test.du.cesnet.cz`. |
| 33 | +5. Select the desired files and click **Import** to bring them into your Galaxy history. |
| 34 | + |
| 35 | +## Step 4: Run a Workflow |
| 36 | + |
| 37 | +1. With the data in your history, you can now run an analysis. |
| 38 | +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](https://galaxyproject.org/learn/g101/workflows/). |
| 39 | +3. Run the workflow on your imported data. |
| 40 | + |
| 41 | +## Step 5: Export Workflow Invocation to the Repository |
| 42 | + |
| 43 | +1. Once the workflow has finished running, you can export the entire workflow invocation, including the results and provenance information. |
| 44 | +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. |
| 45 | +3. Galaxy supports exporting this information in the **RO-Crate** format, which is a standard for packaging research objects. |
| 46 | +4. From the workflow invocation page, click the **Export** button. |
| 47 | +5. In the export wizard, configure the following options: |
| 48 | + - As the format select **Workflow Run RO-Crate**. |
| 49 | + - For the destination select **RDM repository**. |
| 50 | + - For creating the record select repository **CESNET-Invenio TESTING**. |
| 51 | + - Name the record and create it. |
| 52 | + - Finally, export the workflow invocation to the newly created record. |
| 53 | +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. |
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