Installing QuPath on HPC the “easy way”

• Download install_QuPath_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_QuPath_w_download.sh
• Run ./install_QuPath_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)

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 chomd 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