viennarna
Link to section 'Introduction' of '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/.
Link to section 'Versions' of 'viennarna' Versions
- 2.5.0
Link to section 'Commands' of 'viennarna' 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
Link to section 'Module' of 'viennarna' Module
You can load the modules by:
module load biocontainers
module load viennarna
Link to section 'Example job' of 'viennarna' Example job
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