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MSFragger

Ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

Setting up FragPipe on remote Linux server (with X forwarding)

Users can run FragPipe on a remote Linux server with X forwarding. Both of the server and client need to be setup.

For the details of setting up FragPipe itself, please refer to Setting up FragPipe.

Disclaimer: different Linux distributions have different ways to install and setup X forwarding. Thus, instructions below may need to be modified for a particular system.

Setup the remote Linux server

  1. The server needs to have X window related packages. Different distributions have different ways to install those package. Following is an example for Ubuntu:
    sudo apt-get update
    sudo apt-get upgrade
    sudo apt-get install xorg openbox
    
  2. Open /etc/ssh/sshd_config (need root permission), and edit:
    X11Forwarding yes
    X11DisplayOffset 10
    
  3. Restart ssh daemon using sudo service sshd restart

Setup the Windows client on your Windows machine

  1. Download PuTTY from https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html, and install it.
  2. Download Xming from https://sourceforge.net/projects/xming/, and install it.
  3. Make sure that Xming is running in the background. Start Xming by clicking Xming from the Start menu:

  1. Open PuTTY, fill in Host Name (or IP address) and Saved Sessions, then clicking Save.

  1. Click SSH then X11. Then, click Enable X11 forwarding.

  1. (Optional) If you are using private key to login. Click SSH then Auth. Then, fill your private key path in Private key file for authentication.

  1. Go back to Session and click Save again to save your settings.

  1. Click Open to log into your server with user name and password (or private key).

  2. Find your FragPipe and start fragpipe in <FragPipe directory>/bin.

  3. Enjoy!

Setup the Mac client on your Mac machine

  1. Download XQuartz from https://www.xquartz.org/, and install it.
  2. Run Applications -> Utilities -> XQuartz.app
  3. Right click on the XQuartz icon in the dock and select Applications -> Terminal.
  4. In the opened xterm window, log into the server using (replacing username and ip-address to real ones)
    ssh -X username@ip-address
    
  5. Find your FragPipe and start fragpipe in <FragPipe directory>/bin.
  6. Enjoy!