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Compass is an algorithm to characterise the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis (FBA).

Compass is available as a module which wraps an Apptainer container on Apocrita.


To run the default installed version of Compass, simply load the compass module:

$ module load compass
$ compass -help
usage: Compass [-h] [--data FILE] [--data-mtx FILE [FILE ...]] [--model MODEL] [--species SPECIES]
               [--media MEDIA] [--output-dir DIR] [--temp-dir DIR] [--torque-queue QUEUE]
               [--num-processes N] [--lambda F] [--num-threads N] [--and-function FXN]
               [--select-reactions FILE] [--select-subsystems FILE] [--num-neighbors N]
               [--symmetric-kernel] [--input-weights FILE] [--penalty-diffusion MODE] [--no-reactions]
               [--calc-metabolites] [--precache] [--input-knn FILE] [--input-knn-distances FILE]
               [--output-knn FILE] [--latent-space FILE] [--only-penalties] [--example-inputs]
               [--microcluster-size C] [--microcluster-file FILE] [--microcluster-data-file FILE]
               [--anndata-output] [--isoform-summing MODE] [--list-genes FILE] [--list-reactions FILE]

For full usage documentation, run compass --help.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory using the homo_sapiens species:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_vmem=1G
#$ -l h_rt=1:0:0

module load compass

compass --data expression.tsv \
        --num-processes "${NSLOTS}" \
        --species homo_sapiens