Viennarna

Introduction

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

For more information, please check:
BioContainers: https://biocontainers.pro/tools/viennarna
Home page: https://www.tbi.univie.ac.at/RNA/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.5.0

BELL

2.5.0

GAUTSCHI

2.5.0

NEGISHI

2.5.0

SCHOLAR

2.5.0

Commands

  • RNA2Dfold

  • RNALalifold

  • RNALfold

  • RNAPKplex

  • RNAaliduplex

  • RNAalifold

  • RNAcofold

  • RNAdistance

  • RNAdos

  • RNAduplex

  • RNAeval

  • RNAfold

  • RNAforester

  • RNAheat

  • RNAinverse

  • RNAlocmin

  • RNAmultifold

  • RNApaln

  • RNAparconv

  • RNApdist

  • RNAplex

  • RNAplfold

  • RNAplot

  • RNApvmin

  • RNAsnoop

  • RNAsubopt

  • RNAup

  • Kinfold

  • b2ct

  • popt

Module

You can load the modules by:

module load biocontainers
module load viennarna

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run viennarna on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers viennarna

# Your viennarna workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers viennarna

# Your viennarna workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers viennarna

# Your viennarna workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers viennarna

# Your viennarna workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=viennarna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers viennarna

# Your viennarna workflow...