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aggregate_and_plot.sh

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    Timo Millenaar authored
    c9504e82
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    aggregate_and_plot.sh 782 B
    #!/usr/bin/sh
    SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
    cd $SCRIPT_DIR
    TOIL_VENV_DIR="${SCRIPT_DIR}/toil_venv"
    if [ -d "toil_venv" ]; then
        echo "Activating existing virtual environment."
        source "${TOIL_VENV_DIR}/bin/activate"
    else
        echo "Creating new virtual environment for using toil"
        python3.9 -m venv $TOIL_VENV_DIR
        source "${TOIL_VENV_DIR}/bin/activate"
        pip install --upgrade pip setuptools wheel
        pip install toil[cwl] singularity
    fi
    export SINGULARITY_BIND="/project:/project"
    export TOIL_SLURM_ARGS="--exclusive"
    toil-cwl-runner "${SCRIPT_DIR}/imaging_compress_pipeline.git/aggregate_and_plot.cwl" --workdir $SCRIPT_DIR --logDebug --singularity --batchSystem slurm --batchLogsDir ./logs --jobStore ./job_store