gambit
Link to section 'Introduction' of 'gambit' Introduction
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens.
Docker hub: https://hub.docker.com/r/staphb/gambit
Home page: https://github.com/jlumpe/gambit
Link to section 'Versions' of 'gambit' Versions
- 0.5.0
Link to section 'Commands' of 'gambit' Commands
- gambit
Link to section 'Module' of 'gambit' Module
You can load the modules by:
module load biocontainers
module load gambit
Link to section 'Example job' of 'gambit' 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 gambit on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gambit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers gambit
gambit -d database query -o results.csv *.fasta