roary
Link to section 'Introduction' of '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.
Docker hub: https://hub.docker.com/r/staphb/roary
Home page: https://github.com/sanger-pathogens/Roary
Link to section 'Versions' of 'roary' Versions
- 3.13.0
Link to section 'Commands' of 'roary' Commands
- roary
Link to section 'Module' of 'roary' Module
You can load the modules by:
module load biocontainers
module load roary
Link to section 'Example job' of 'roary' 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 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