Open OnDemand is a suite of software that provides a graphical web interface to HPC resources and other interactive research computing applications. RELION is a software package for analyzing Cryo Electron Microscopy (Cryo-EM) data. The purpose of this document is to demonstrate how to run the RELION software in an interactive desktop in Open OnDemand.
Lines beginning with $ indicate shell commands. You may type these manually, or copy/paste them from this document. Either way, do not include the $ when executing commands. Text below commands indicates expected output.
1. Login to the Open OnDemand portal and launch an interactive desktop session on Thunder. Once the session is running, open the graphical desktop window.
2. Working in the virtual desktop, open the terminal application by clicking the icon on the dock at the bottom of the screen.
$ cd /gpfs1/scratch/first.lastname
$ mkdir relion-test
$ cd relion-test
$ module load intel impi relion
Only run the relion GUI from your ProjectDirectory. Do you want to start a new project here [y/n]? y