Installing FIJI on HPC the “easy way”

• Download install_FIJI_w_download.sh into a folder in your nemo space to which you want to install FIJI
• Open up an OnDemand 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_FIJI_w_download.sh
• Run ./install_FIJI_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_Fiji.sh

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