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Commit 54688ca7 authored by Tim Roloff Handschin's avatar Tim Roloff Handschin
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Update abricate_exercise.md

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exercises/abricate_exercise.md
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...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
<https://github.com/tseemann/abricate> <https://github.com/tseemann/abricate>
### Check for available databases ### Check for available databases in an interactive session
- Abricate can search various databases (even custom built). - Abricate can search various databases (even custom built).
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l
module load singularityce module load singularityce
srun /shares/amr.imm.uzh/bioinfo/singularity/quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img abricate --list srun /shares/amr.imm.uzh/bioinfo/singularity/sandbox/abricate_1.0.1 abricate --list
- This will generate the following output - This will generate the following output
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ecoli_vf 2701 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27
vfdb 2597 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27
- **Close your interactive session** before you continue
### Screen your genomes for resistance genes and virulence factors ### Screen your genomes for resistance genes and virulence factors
- **How to run abricate:** - **How to run abricate:**
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