Introduction

Usage

module load anaconda3/2019.07py3
source activate cellprofiler

Sample pbs script

#!/bin/bash
#PBS -N condatest
#PBS -m abe
#PBS -M yourEmail@alumni.griffithuni.edu.au
#PBS -l select=1:ncpus=4:mpiprocs=4:mem=10gb,walltime=10:00:00
##ilastik will by default use all cores. It needs to be restricted with the following
export LAZYFLOW_THREADS=4
export LAZYFLOW_TOTAL_RAM_MB=8000
#
cd  $PBS_O_WORKDIR
module load anaconda3/2019.07py3
source activate cellprofiler
#module load misc/fiji/fiji
#module load misc/imagej/152
module load mpi/mpich-3.2-x86_64
export INPUTDIR=/export/home/s12345/pbs/data/ExampleTumor/images
export OUTPUTDIR=/export/home/s12345/pbs/data/ExampleTumor/output
export PIPELINE=/export/home/s12345/pbs/data/ExampleTumor/ExampleTumor.cppipe
cellprofiler  --do-not-build --do-not-fetch -r -c  -i "$INPUTDIR" -o "$OUTPUTDIR" -p "$PIPELINE"  -d cpdone.txt

Reference

https://portal.biohpc.swmed.edu/content/guides/cellprofiler-biohpc/