Installing QuPath (version 0.5.1) on HPC the “easy way”

• Download install_QuPath5.1_w_download.sh into a folder in your nemo space to which you want to install QuPath
• Open up an OnDemand GPU Desktop. For instructions on how to do this, see [this documentation].
• Open up a terminal in OnDemand (right click anywhere on the screen and open up xterm)
• Navigate to the folder on Nemo in which you put install_QuPath5.1_w_download.sh
• Run ./install_QuPath5.1_w_download.sh – This will install the program, and create a new run script in your top level home directory
• Start a new xterm (or type in cd $HOME)

• type in ./Run_QuPath.sh

• At anypoint you want to run QuPath, you can run the script ./RunQuPath.sh from your home directory (the first directory that opens when you start xterm)

• If you encounter an error when trying to run the installation script, it is likely due to the script not having execute permissions. To resolve this issue, run the following command

     chmod +x install_QuPath5.1_w_download.sh
  

• Verify the x (‘execute’) permission is now present by running:

    ls -l install_QuPath5.1_w_download.sh
  

  Now, try running the script again:

  ./install_QuPath5.1_w_download.sh

Installing QuPath in your working directory (The harder way)

• Download QuPath for Linux and put it in your working directory on nemo. It will have a file extension of .tar.xz
• Open up an OnDemand GPU Desktop. For instructions on how to do this, see [this documentation].
• Open up a terminal in OnDemand (right click anywhere on the screen and open up xterm)
• Navigate to the folder on Nemo in which you put the QuPath installation file (this is /path/to/QuPath)
• use the command tar -xf QuPath-******.tar.xz Where the ***** represents the version of QuPath
• use the command chmod u+x /path/to/QuPath/bin/QuPath to change the permissions of the launcher
• Navigate to the folder /path/to/QuPath/bin/ and type in ./QuPath to run QuPath