diff --git a/exercises/abricate_exercise.md b/exercises/abricate_exercise.md index 7cf703d839910a5c38203c57219bbcc5df9ae30a..18ab12408d00eda35339fe1b082befe9adccda45 100644 --- a/exercises/abricate_exercise.md +++ b/exercises/abricate_exercise.md @@ -10,7 +10,8 @@ - Abricate can search various databases (even custom built). -- We can write a script to check which databases are installed and available using `abricate --list` We can also run that in an interactive session using the code below: +- We can write a script to check which databases are installed and available using `abricate --list` + We can also run that in an interactive session using the code below: srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l module load singularityce @@ -27,13 +28,13 @@ Add the following parameters `--quiet --nopath --db [DATABASE]` - Use the databases `ncbi` and `vfdb` + Run abricate twice, once on `ncbi` and once `vfdb` The Singularity image can be found at /shares/amr.imm.uzh/bioinfo/singularity7quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img - Use following SLURM parameters: + Use the following SLURM parameters: #!/usr/bin/env bash #SBATCH --time=01:00:00