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martenson merged 2 commits into from
Dec 12, 2025
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include first version of documentation for cesnet invenio integration #68

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add a page describing the process of importing from and exporting to NRP
martenson Dec 11, 2025
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53 changes: 53 additions & 0 deletions content/docs/graphical/galaxy-nrp-integration.mdx
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---
title: Using Galaxy in combination with NRP repositories
---

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)).

# 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/](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/](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](https://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](https://galaxyproject.org/learn/g101/workflows/).
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.
1 change: 1 addition & 0 deletions content/docs/graphical/usegalaxy.mdx
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## References and Use Cases

* [Presentation from MetaCenter HPC Seminar 9/2025](https://metavo.metacentrum.cz/export/sites/meta/cs/seminars/Seminar2025/Krenek_Galaxy_metausers_2025.pdf)
* [National Repository Platform (NRP) Integration](/docs/graphical/galaxy-nrp-integration)

Those video tutorials were given at the EOSC Symposium 2025:
* [4 different Communities (Bio, Astro, Earth, Climate) doing Imaging data analysis in Galaxy](https://gxy.io/eosc25)
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