We have two versions of Qiime2 available, version 2026.4 and 2026.7 via our containerized software platform.
You can load them via the module system
module avail
module load qiime/2026.7
This will also load apptainer.
An SBATCH script would look like the following (replace UID with your username):
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18 | #!/bin/bash
#SBATCH -J 'qiime2 analysis' # Job name
#SBATCH -o /work/<<UID>>/job.%j.out # Name of stdout output file (%j expands to jobId)
#SBATCH -e /work/<<UID>>/job.%j.err # Name of stderr output file (%j expands to jobId)
#SBATCH -n 16 # Total number of threads requested or total number of mpi tasks
#SBATCH --mem=32000 # Maximum amount of memory in Mb the job can use.
#SBATCH -t 04:00:00 # Run time ([d-]hh:mm:ss) - 4 hours
#SBATCH --mail-type=ALL
#SBATCH --mail-user=your.email@wur.nl
# Load your software/command
module load qiime/2026.7
# Run your command
qiime metadata tabulate \
--m-input-file sample-metadata.tsv \
--o-visualization sample-metadata-viz.qzv
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