1) Do not run Crux on the 'tephra' head node of our cluster. You should 'ssh' into sage (Genome Sciences department cluster front end) or tephra (UWPR cluster front end) and then type 'qlogin'. This will get you a shell on a cluster node with more resources (memory/CPU) than the head nodes. 2) You will need to setup your environment to run Crux version 2.1. This entails subscribing to different software using the module command. Run the following module command: module load modules modules-init modules-gs/prod gmp/latest mpfr/latest mpc/latest gcc/latest As a shortcut, paste these commands into your .bashrc file. 2) The binary is named 'crux'. Type that without arguments to see the usage statement. You'll likely run commands like crux spectral-count ... crux percolator ... crux tide-search ... crux comet ... 3) You can find Crux documentation and tutorials here. 4) For Crux questions, ask them on the mailing list here.