The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

References:

• http://dx.doi.org/10.1186/1748-7188-6-26

• https://www.tbi.univie.ac.at/RNA/#

• Module Name: viennarna (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load viennarna
[user@cn3144 ~]$ RNAfold -h

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load viennarna
RNAfold < INPUT.fa

Submit this job using the Slurm sbatch command.

sbatch batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; RNAfold < INPUT.fa
cd dir2; RNAfold < INPUT.fa
cd dir3; RNAfold < INPUT.fa

Submit this job using the swarm command.

swarm -f job.swarm --module viennarna