Circlator

Introduction

Circlator is a tool to circularize genome assemblies.

For more information, please check its | Docker hub: https://hub.docker.com/r/sangerpathogens/circlator and its home page on Github.

Versions

• 1.5.5

Commands

• circlator

• python3

Module

You can load the modules by:

module load biocontainers
module load circlator

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 Circlator on our clusters:

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

module --force purge
ml biocontainers circlator

circlator minimus2  minimus2_test_run_minimus2.in.fa  minimus2_test