staramr
Link to section 'Introduction' of 'staramr' Introduction
staramr scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes.
Docker hub: https://hub.docker.com/r/staphb/staramr
Home page: https://github.com/phac-nml/staramr
Link to section 'Versions' of 'staramr' Versions
- 0.7.1
Link to section 'Commands' of 'staramr' Commands
- staramr
Link to section 'Module' of 'staramr' Module
You can load the modules by:
module load biocontainers
module load staramr
Link to section 'Example job' of 'staramr' 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 staramr on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=staramr
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers staramr
staramr db info
staramr search \
--pointfinder-organism salmonella \
-o out *.fasta