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):

    #!/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