## Helper scripts for setting up, submitting and analyzing cafemol runs

## Usage: Copy the scripts_folder  to a desired path and 
###        Run: bash setup.sh path_to_scripts_folder
#
1. Copy the scripts folder to a desired path, the full path to the scripts folder will be referred as script_path
   Set up the enrironment variables in the setup.sh file
   Specify the paths to Cafemol and Xplor in the setup.sh file 
   Run: bash setup.sh script_path 
2. The usage of each script is explained in the protocol.txt file
3. Three folders calculation, analysis, and analysis2 contain various executable scripts for Cafemol
   templates folder contains template files for Cafemol run
   cg2aa folder contains script for glob to all atom conversion
   cafemol_3.2.0.mod folder is the cafemol package that needs to be compiled by the user
   rna2d3d folder contains scripts for conversion of 2D base pair information into open 3D RNA conformation,
   the singularity executable rna2d3d-biowulf.simg is from Shapiro Lab.
   utility folder conatins other helpful scripts
4. Main dependencie:
                    OS: Red Hat Enterprise Linux Server release 7.9
                    Job scheduler: SLURM
                    Packages: cafemol/3.2.0, Python/3.5, R/4.0, Xplor-NIH/3.4
