Step 1: Uncompress and set up the environment variables

a) uncompress the tar file using "tar -zxvf RS3D.tgz"
b) change directory to bin using "cd RS3D/bin"
c) Define the environment variables in the RS3D_SETUP.sh file
   run the command "source RS3D_SETUP.sh"

d) Bind your directories for singulaity (http://singularity.lbl.gov/docs-mount)
   Modify the line starting with "export SINGULARITY_BINDPATH=" in the file /RS3D/bin/qsub-rna2d3d to include your HPC directories

Step 2: Compile RS3d source code

Go to the directory RS3D/src 
run the command "make" in your terminal
To invoke intel compiler, run the command "make run.icpc-omp"
NOTE: If you have any issues compiling RS3D, we have also provided a singularity image named
"rs3d-COS.simg". You can skip this compilation step, and use the given singularity file instead
by specifying "self.processing_script = "qsub-run-sing"" in the line starting with "self.processing_script"
in the RS3D.py file.

Step 3: Platform specific change 
You may need to change the varible "SCRATCH_DIR" in the file "RS3D/bin/qsub-run-gcc" 
to whatever scratch space your HPC system uses.
Do the same for the file "RS3D/bin/qsub-run-icpc" if your are using the icpc compiler.
Do the same for the file "RS3D/bin/qsub-run-sing" and modify the SINGULARITY_BINDPATH 
as described in setp 1, if you want to skip the compilation step 2 and instead use the singularity file.

Replace the variable “SLURM_JOBID” with an equivalent variable in the file “RS3D/bin/utils.sh”.