###########
 Viennarna
###########

**************
 Introduction
**************

Viennarna is a set of standalone programs and libraries used for
prediction and analysis of RNA secondary structures.

**********
 Versions
**********

-  2.5.0

**********
 Commands
**********

-  b2ct
-  Kinfold
-  popt
-  RNA2Dfold
-  RNAaliduplex
-  RNAalifold
-  RNAcofold
-  RNAdistance
-  RNAdos
-  RNAduplex
-  RNAeval
-  RNAfold
-  RNAforester
-  RNAheat
-  RNAinverse
-  RNALalifold
-  RNALfold
-  RNAlocmin
-  RNAmultifold
-  RNApaln
-  RNAparconv
-  RNApdist
-  RNAPKplex
-  RNAplex
-  RNAplfold
-  RNAplot
-  RNApvmin
-  RNAsnoop
-  RNAsubopt
-  RNAup

*************
 Example job
*************

Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=viennarna   # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load viennarna/XXXX     ### Latest version is recommended.