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SFTP File Transfer Clients

This page provides instructions for setting up graphical SFTP clients to transfer files to and from the XLence cluster.

Use case: Download NGS data, upload input files, transfer results to your local computer.

Cyberduck (Windows, macOS)

Cyberduck is a free, open-source file transfer client available for Windows and macOS.

Installation

Download from: https://cyberduck.io/

Setup

  1. Open Cyberduck

  2. Click "Open Connection" (top-left)

  3. Configure connection:

  4. Protocol: SFTP (SSH File Transfer Protocol)
  5. Server: xlence.disfeb.unimi.it
  6. Port: 22
  7. Username: Your XLence username

  8. Password: Your XLence password

  9. Click "Connect"

  10. Browse and transfer files:

  11. Drag and drop files between windows
  12. Right-click for options (download, upload, delete)

Bookmarks

Save the connection for quick access: - After connecting, click Bookmark → New Bookmark - The connection will appear in your bookmarks list

FileZilla (Windows, macOS, Linux)

FileZilla is a popular free FTP/SFTP client available on all platforms.

Installation

Download from: https://filezilla-project.org/

Important: Download the FileZilla Client (not Server)

Setup

  1. Open FileZilla

  2. Configure connection:

  3. Host: sftp://xlence.disfeb.unimi.it
  4. Username: Your XLence username
  5. Password: Your XLence password

  6. Port: 22

  7. Click "Quickconnect"

  8. Accept host key (first time only)

  9. Transfer files:

  10. Left panel: Your local computer
  11. Right panel: XLence cluster
  12. Drag and drop files between panels

Site Manager (Save Connection)

To save the connection for future use:

  1. Click File → Site Manager
  2. Click New Site
  3. Configure:
  4. Protocol: SFTP - SSH File Transfer Protocol
  5. Host: xlence.disfeb.unimi.it
  6. Port: 22
  7. Logon Type: Normal
  8. User: Your username
  9. Click Connect

WinSCP (Windows Only)

WinSCP is a Windows-only SFTP/SCP client with advanced features.

Installation

Download from: https://winscp.net/

Setup

  1. Open WinSCP

  2. Login dialog appears automatically

  3. Configure connection:

  4. File protocol: SFTP
  5. Host name: xlence.disfeb.unimi.it
  6. Port number: 22
  7. User name: Your XLence username

  8. Password: Your XLence password

  9. Click "Login"

  10. Accept host key (first time only)

  11. Transfer files:

  12. Left panel: Local computer
  13. Right panel: Cluster
  14. Drag and drop, or use toolbar buttons

Save Connection

  • Click Save before connecting
  • The site will appear in the login dialog for quick access

Commander Interface

WinSCP offers a dual-pane interface similar to file managers: - Easy to navigate both local and remote filesystems - Integrated text editor for quick file edits

Downloading NGS Data

Locating Your Data

NGS sequencing data is typically stored in:

/path/to/ngs/data/your_project/

Contact administrators for the exact path to your data.

Download Process

  1. Connect to the cluster using one of the clients above

  2. Navigate to your NGS data directory:

  3. Browse to /path/to/ngs/data/

  4. Find your project folder

  5. Select files to download:

  6. FASTQ files (.fastq, .fastq.gz)
  7. Analysis results

  8. Quality control reports

  9. Download:

  10. Drag files to your local computer

  11. Or right-click → Download

  12. Verify download:

  13. Check file sizes match
  14. Verify data integrity (see below)

Large Dataset Tips

For very large NGS datasets (>10 GB):

  • Use resume capability: Most clients support resuming interrupted transfers
  • Download overnight: Large transfers may take hours
  • Check disk space: Ensure you have sufficient local storage
  • Compress first (optional): On the cluster, compress with tar -czf project.tar.gz directory/ before downloading

Verifying Data Integrity

After downloading important data, verify integrity:

Using Checksums

On the cluster (via SSH):

md5sum your_file.fastq.gz > checksums.txt

On your local computer:

# Linux/macOS
md5sum your_file.fastq.gz

# Windows PowerShell
Get-FileHash -Algorithm MD5 your_file.fastq.gz

Compare the checksums to ensure successful transfer.

Troubleshooting

Connection Refused

  • Verify hostname: xlence.disfeb.unimi.it
  • Check your internet connection
  • Ensure you're using port 22

Authentication Failed

  • Double-check your username and password
  • Verify your account is active
  • Contact administrators if issues persist

Slow Transfers

  • Network congestion: Try at different times
  • Large files: Be patient, transfers may take hours
  • Use compression for multiple small files

Permission Denied

  • Check you have read access to the directory
  • Contact administrators for access to restricted data

Support

For questions about file transfers or accessing data:

Last Updated: October 2025