esm.def

Bootstrap: library
From: ubuntu:18.04

%post
    # Here we put scripts to run immediatley after initialisation of the OS

    # Update Ubuntu package repos
    echo "deb http://gb.archive.ubuntu.com/ubuntu bionic main restricted" >> /etc/apt/sources.list
    echo "deb http://gb.archive.ubuntu.com/ubuntu bionic universe" >> /etc/apt/sources.list
    echo "deb http://gb.archive.ubuntu.com/ubuntu bionic-updates multiverse" >> /etc/apt/sources.list
    echo "deb http://gb.archive.ubuntu.com/ubuntu bionic-backports main restricted universe multiverse" >> /etc/apt/sources.list
    echo "deb http://gb.archive.ubuntu.com/ubuntu bionic-security main restricted" >> /etc/apt/sources.list

    # Install packages
    apt-get update
    apt-get install -y libssl-dev libgsl-dev libxml2-dev libcurl4-openssl-dev git r-base r-base-dev r-cran-littler r-cran-rjags r-cran-curl r-cran-car r-cran-mvtnorm r-cran-mcmcpack r-cran-openssl r-cran-xml2 pandoc
  
    # Clone git repository
    git clone https://github.com/oxacclab/ExploringSocialMetacognition ESM
    
    # Run setup R script
    r /ESM/analysis/ACv2/src/install-packages.R
  
%runscript
    NOW=$(date)
    # Commands to run when called
    echo "Container created $NOW"
    
    # Parse arguments
    GIT=""
    TIME=""
    FILE="ACv2/directBenevolenceContext_v0.0.1"
    VERBOSE=$false
    
    while getopts ":g:t:f:v" opt; do
        case ${opt} in
            g ) 
                GIT=$OPTARG
                ;;
            t )
                TIME=$OPTARG
                ;;
            f )
                FILE=$OPTARG
                ;;
            v )
                VERBOSE=$true
                ;;
            \? )
                echo "Invalid Option: -$OPTARG" 1>&2
                exit 1
                ;;
            : )
                echo "Invalid Option: $OPTARG requires an argument" 1>&2
                exit 1
                ;;
        esac
    done
    
    echo "Arguments parsed with getopts"
    
    # Look up GIT argument if a date and extract most recent commit given that date
    if [ "$TIME" != "" ]; then
        echo "TIME variable set"
        if [ "$GIT" != "" ]; then
            echo "GIT variable set"
            echo "You cannot specify both a -t and -g argument."
            exit 1
        fi
        
        # TIME=date --date="$TIME" --iso-8601=seconds
        echo "Finding first commit made prior to $TIME"
        cd /ESM
        GIT=$(git rev-list -n 1 --before="$TIME" master)
    fi
    
    
    if [ "$GIT" != "" ]; then
        cd /ESM
        git checkout $GIT
        echo "GIT:    $GIT"
    fi
      
    if [ "$TIME" != "" ]; then
        echo "(By TIME:   ${TIME})"
    fi
    
    echo "FILE:   $FILE"
    if [ $VERBOSE ]; then
        echo "VERBOSE:    TRUE"
    fi
    
    if [ "$FILE" != "" ]; then
        # Knit and return a specific file
    
        echo "Knitting analysis script..."
        R=rmarkdown::render\(\"/ESM/analysis/${FILE}.Rmd\"\)
        echo $R
        
        # r -e $R
    
        # cat /ESM/analysis/${FILE}.html
    fi
    
%test
    # Check whether R installed properly
  
%labels
    Author matt.jaquiery@psy.ox.ac.uk
    Version v0.0.2
    Date 2019-12-29
  
%help
    This container should provide a reproducible version of the study at a given point in its history. It should provide a useable version of the study on a local webserver, and access to the analysis scripts run in an environment identical to the one used for the write-up of the project. 
    By default it will print out an HTML file freshly generated from Rmarkdown code.