Practical guide for using Nextcloud for secure data storage, sharing, collaboration, and integration with research workflows.
Edit me

Nextcloud is a secure cloud platform for managing and sharing research data at Würzburg University. This guide provides step-by-step instructions to register, sync and share data, collaborate using Office tools, and connect your data to analysis servers using rclone.

1. Registration and Login

A. Register and Log In

2. Upload and Download Files

A. Upload via Browser

  1. Log in to the web interface.
  2. Click the “+” icon → Upload File or Upload Folder.
  3. Or drag-and-drop files directly into your folder structure.

B. Download Files

  1. Right-click on any file or folder.
  2. Select Download to retrieve a ZIP archive or the individual file.

3. Synchronize with the Desktop or Mobile Client

A. Install the Nextcloud Client

B. Set Up Synchronization

  1. Launch the client after installation.
  2. Server address: https://www.coreunitrdm.biozentrum.uni-wuerzburg.de/
  3. Enter your username and password.
  4. Choose folders to sync locally.

💡 Tip: Use selective sync to save space when handling large datasets.

4. Share Data Securely

  1. Click the Share icon beside a file or folder.
  2. Create a public link.
  3. Configure access:
    • Password protection
    • Expiration date
    • Download or upload permissions

B. Share with Specific Users

  1. Enter the user’s name or email.
  2. Set specific access levels: view, edit, upload, or delete.

🔗 Official File Sharing Guide

5. Customize File Access Rights

  • Click the Share icon → then the three-dot menu (⋮) next to a user or link.
  • Adjust:
    • Edit or view-only access
    • Download visibility
    • Resharing rights
    • Expiration date

🔗 Advanced Access Rights (ACLs)

6. Use OnlyOffice in Nextcloud

You can edit Microsoft Office files directly in the browser:

  1. Click on any .docx, .xlsx, or .pptx file.
  2. It opens in OnlyOffice.
  3. Collaborate live with colleagues.
  4. Add comments and track changes.

7. Restore Deleted Files or Previous Versions

A. Restore Deleted Files

  • Open the Deleted Files tab in the left sidebar.
  • Click Restore to recover a file or folder.

B. Restore Previous Versions

  • Hover over a file → click the three-dot menu (⋮) → choose Versions.
  • Select and restore the desired version.

8. Connect to Analysis Servers Using rclone

You can mount or transfer data from Nextcloud directly to an HPC or remote server using rclone + WebDAV.

🔗 rclone WebDAV Documentation

A. Install rclone

sudo apt install rclone

B. Configure a New Remote

rclone config
  • Choose n for new remote
  • Name it: nextcloud
  • Type: webdav
  • URL: https://www.coreunitrdm.biozentrum.uni-wuerzburg.de/remote.php/dav/files/YOURUSERNAME/
  • WebDAV type: Nextcloud
  • Enter your username and an App Password (generate it in Settings → Security → App Passwords)

C. Use rclone to Mount or Copy Files

Mount your Nextcloud folder:

rclone mount nextcloud:/ ~/mnt/nextcloud --vfs-cache-mode writes

Copy files to/from Nextcloud:

rclone copy /local/folder nextcloud:/your-folder --progress

🔐 App passwords are safer than your login credentials and can be revoked at any time.

9. Need Help?

Johannes Balkenhol
Chair of Bioinformatics, University of Würzburg
✉️ johannes.balkenhol@uni-wuerzburg.de
🌐 https://www.biozentrum.uni-wuerzburg.de/bioinfo/

Tags: