Running Crux at UWPR

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.
   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. 

   Next, log into a cluster node and request 14GB free memory (tephra nodes have 16GB total RAM):

      qlogin -l h_vmem=14G

2) The binary is named 'crux'.  Type that without arguments to see the usage statement.

   To see what version of Crux is installed (verion 3.0.17109 currently), you can type:

      crux -version

   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.