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 its website: https://biocontainers.pro/tools/viennarna and its home page: https://www.tbi.univie.ac.at/RNA/.
Versions
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 -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
ml biocontainers viennarna
RNAfold < test.seq
RNAfold -p --MEA < test.seq