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.
- 1.5.5
Commands ~~~~~~~ - circlator - python3
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