Accessing GW Remotely

GW supports multiple methods for accessing and visualizing data over remote connections. This guide covers the available approaches and their recommended use cases.

Direct Remote Data Access

GW can directly access remote data through HTTP/HTTPS or FTP protocols. Simply provide the full URL path (starting with http:// or ftp://) to your data files, and GW will attempt to load them from your local machine.

Secure Access Methods

For data requiring secure access (e.g., SSH authentication), you have several options:

1. SSHFS Mount Method

SSHFS allows you to mount remote directories to your local filesystem, enabling GW to access remote files as if they were local.

Platform-Specific Setup:

Advantages:

  • Simple to use once configured
  • Transparent access to remote and local files
  • No modification to GW usage required

2. X11 Forwarding

Run GW on a remote server while displaying the interface on your local machine.

ssh -X username@remote-server
gw --delay 100  # Add delay to handle latency

Important Notes:

  • Works best between Linux systems
  • Mac-to-Linux connections mostly do not work (you may be lucky)
  • Use the --delay parameter (in milliseconds) to handle latency issues

3. Xpra

Xpra offers superior performance compared to X11 forwarding, especially for graphical applications.

Setup Instructions:

  1. Install Xpra on both local and remote machines
  2. Start GW on the remote machine: 
    xpra start :100 --start="gw ref.fa -b your.bam -r chr1:50000-60000" --sharing=yes --daemon=no
  3. Connect from your local machine: 
    xpra attach ssh:username@remote-server:100

For custom SSH configurations:

xpra attach ssh:username@remote-server:100 --ssh "ssh -o IdentitiesOnly=yes -i /path/to/key.pem"

Key Features:

  • Better performance than X11
  • Supports multiple simultaneous users
  • More resilient to network issues

4. VNC Access

For a full remote desktop experience, consider using VNC (e.g., TigerVNC).

Note: This method requires administrator setup on the remote server.

Comparison of Methods

Method Performance Setup Complexity Best For
SSHFS Good Low Direct file access
X11 Fair Low Quick access, Linux-to-Linux
Xpra Excellent Medium Regular remote usage
VNC Good High Full desktop access

Graphics and Display Issues

Testing OpenGL Support

  1. Check OpenGL capabilities using glxinfo: 
    glxinfo | grep "direct rendering"
glxinfo | grep "OpenGL version"

If these commands aren’t available, install them:

  • Ubuntu/Debian: sudo apt-get install mesa-utils
  • RHEL/CentOS: sudo yum install glx-utils

Expected output should show:

  • “direct rendering: Yes”
  • OpenGL version 2.0 or higher

Testing Graphics Performance

Use glxgears to test basic 3D rendering:

glxgears -info

This will display rotating gears and report FPS (Frames Per Second). Low FPS (<30) may indicate:

  • Graphics driver issues
  • X11 forwarding bandwidth limitations
  • Hardware acceleration problems

Common Issues and Solutions

  1. Blank or Black Window
    • Check OpenGL support using methods above
    • Try forcing software rendering: 
      export LIBGL_ALWAYS_SOFTWARE=1
  2. Slow Performance
    • For X11: Increase delay value 
      gw --delay 200  # Adjust value as needed
    • For Xpra: Use compression options 
      xpra start :100 --encoding=rgb --compress=0
  3. Connection Refused
    • Verify SSH access: 
      ssh -v username@remote-server
    • Check if X11 forwarding is enabled in /etc/ssh/sshd_config: 
      X11Forwarding yes
  4. Display Export Errors
    • Ensure DISPLAY variable is set: 
      echo $DISPLAY
    • Set if missing: 
      export DISPLAY=:0

Getting Help

If problems persist please raise an issue:

  1. Collect system information: 
    gw --version
GW_DEBUG=1 gw hg19 
glxinfo
echo $DISPLAY