pbptyper
Link to section 'Introduction' of 'pbptyper' Introduction
pbptyper is a tool to identify the Penicillin Binding Protein (PBP) of Streptococcus pneumoniae assemblies.
Docker hub: https://hub.docker.com/r/staphb/pbptyper
Home page: https://github.com/rpetit3/pbptyper
Link to section 'Versions' of 'pbptyper' Versions
- 1.0.4
Link to section 'Commands' of 'pbptyper' Commands
- pbptyper
Link to section 'Module' of 'pbptyper' Module
You can load the modules by:
module load biocontainers
module load pbptyper
Link to section 'Example job' of 'pbptyper' 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 pbptyper on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pbptyper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers pbptyper
pbptyper --assembly test/SRR2912551.fna.gz --outdir output