From b0b19c1dd806e9cc8c31647d7be8095cbe2ce8af Mon Sep 17 00:00:00 2001
From: Tim Roloff Handschin <troloff@imm.uzh.ch>
Date: Thu, 30 Mar 2023 14:42:44 +0200
Subject: [PATCH] Replace abricate_exercise.md
---
exercises/abricate_exercise.md | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/exercises/abricate_exercise.md b/exercises/abricate_exercise.md
index 7cf703d..18ab124 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
--
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