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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)