BiSDL.def

Bootstrap: docker
From: ubuntu:20.04
Stage: build

%post

    ln -fs /usr/share/zoneinfo/Europe/Rome /etc/localtime
    export DEBIAN_FRONTEND=noninteractive
    echo "export DEBIAN_FRONTEND=noninteractive" >> $SINGULARITY_ENVIRONMENT

    apt-get update
    apt-get install -y --no-install-recommends apt-utils wget git-all
    
    # Install R, Python, misc. utilities
     
    apt-get install -y python3 python3-pip python3-dev graphviz

    apt-get upgrade -y

    # Install required Python packages
   
    pip3 --no-cache-dir install numpy==1.23.5
    pip3 --no-cache-dir install matplotlib==3.7.1
    pip3 --no-cache-dir install pandas==1.5.3
    pip3 --no-cache-dir install antlr4-python3-runtime==4.9.2

    pip3 install -e git+https://github.com/smilies-polito/nwn-snakes.git#egg=snakes

    apt-get clean
    apt-get update -y
    
    
%runscript
    
    #!/bin/sh
    echo "Compiling BiSDL descriptions into nwn-snakes models for case study: $1"
    python3 bisdl2snakes.py examples/$1/$1.bisdl

    if [ $1 = "bacterial_consortium" ]; then

        echo "Starting petrisim simulation for case study: $1; experimental condition: noLacI; simulation steps: 300"
        python3 run_simulation.py $1 noLacI 300

        echo "Starting petrisim simulation for case study: $1; experimental condition: lowLacI; simulation steps: 300"
        python3 run_simulation.py $1 lowLacI 300

        echo "Starting petrisim simulation for case study: $1; experimental condition: highLacI; simulation steps: 300"
        python3 run_simulation.py $1 highLacI 300

    fi

    if [ $1 = "rgb" ]; then

        echo "Starting petrisim simulation for case study: $1; simulation steps: 60"
        python3 run_simulation.py $1 rgb 60

    fi

    if [ $1 = "pt" ]; then

        echo "Starting petrisim simulation for case study: $1; simulation steps: 60"
        python3 run_simulation.py $1 pt 60

    fi