Roary

Introduction

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/roary

Home page: https://github.com/sanger-pathogens/Roary

Versions

• 3.13.0

Commands

• roary

Module

You can load the modules by:

module load biocontainers
module load roary

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 roary on our clusters:

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

module --force purge
ml biocontainers roary

roary -f demo -e -n -v gff/*.gff