r-session-complete.sdef

Bootstrap: docker
From: ubuntu:focal 

# needed if you want to set up CRAN and BioConductor repos from RSPM (optional)
# set binaryflag to "" in order to stick to source RPMs
%files
    ../scripts/run.R /
    ../scripts/bioc.txt /
    ../scripts/r-packages.txt /

%post -c /bin/bash

    # Install Pro Drivers

    apt-get update && apt-get install -y gdebi-core curl wget
    curl -O https://cdn.rstudio.com/drivers/7C152C12/installer/rstudio-drivers_{{ PRO_DRIVERS_VERSION }}_amd64.deb && \
        gdebi -n rstudio-drivers_{{ PRO_DRIVERS_VERSION }}_amd64.deb && \
        rm -f rstudio-drivers_{{ PRO_DRIVERS_VERSION }}_amd64.deb

    # Install TeXlive 

    apt-get install libpod-simple-perl -y
    curl -LO https://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz && \
        tar xvfz install-tl-unx.tar.gz && \
        rm install-tl-unx.tar.gz && \
        cd install-tl-* && \
        ./install-tl --scheme small --no-interaction

    echo "export PATH=/usr/local/texlive/2024/bin/x86_64-linux:\$PATH" > /etc/profile.d/texlive.sh

    
    # Install Quarto

    curl -o quarto.tar.gz -L https://github.com/quarto-dev/quarto-cli/releases/download/v{{ QUARTO_VERSION }}/quarto-{{ QUARTO_VERSION }}-linux-amd64.tar.gz \
    && mkdir -p /opt/quarto/{{ QUARTO_VERSION }} \
    && tar -zxf quarto.tar.gz -C "/opt/quarto/{{ QUARTO_VERSION }}" --strip-components=1 \
    && rm -f quarto.tar.gz \
    && ln -s /opt/quarto/{{ QUARTO_VERSION }}/bin/quarto /usr/local/bin/quarto

    # Install Python 

    for PYTHON_VERSION in {{ PYTHON_VERSION_LIST }}
    do
        curl -O https://cdn.rstudio.com/python/ubuntu-2004/pkgs/python-${PYTHON_VERSION}_1_amd64.deb
        gdebi -n python-${PYTHON_VERSION}_1_amd64.deb
        rm -f python-${PYTHON_VERSION}_1_amd64.deb
    done

    # Configure Python versions to have 
    #  - upgraded pip 
    #  - configure pip to use posit package manager 
    #  - preinstalling packages needed for the integration with other tools (e.g Connect) 
    # Note: Install will run in parallel to speed up things

    cat << EOF > /etc/pip.conf
[global]
timeout = 60
index-url = https://packagemanager.posit.co/pypi/latest/simple
EOF

    for PYTHON_VERSION in {{ PYTHON_VERSION_LIST }}
    do
        /opt/python/${PYTHON_VERSION}/bin/pip install --upgrade \
            pip setuptools wheel && \
        /opt/python/${PYTHON_VERSION}/bin/pip install \
            ipykernel \
            jupyter \
            rsconnect_jupyter \
            rsconnect_python \
            rsp_jupyter \
            jupyterlab~=4.2.4 \
            pwb_jupyterlab~=1.0 && \
        /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter && \
        /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter && \
        /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter && \
        /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter && \
        /opt/python/${PYTHON_VERSION}/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter && \
        /opt/python/${PYTHON_VERSION}/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" & 
    done
    wait

    # Use default version to point to jupyter and python 
    if [ ! -z {{ PYTHON_VERSION_DEFAULT }} ]; then
        ln -s /opt/python/{{ PYTHON_VERSION_DEFAULT }}/bin/jupyter /usr/local/bin
        ln -s /opt/python/{{ PYTHON_VERSION_DEFAULT }}/bin/python /usr/local/bin
        ln -s /opt/python/{{ PYTHON_VERSION_DEFAULT }}/bin/python3 /usr/local/bin
    fi

    # Install PWB session components 

    mkdir -p /usr/lib/rstudio-server

    DEBIAN_FRONTEND=noninteractive apt-get install -y curl libcurl4-gnutls-dev libssl-dev libuser libuser1-dev rrdtool libpq5

    curl -O https://s3.amazonaws.com/rstudio-ide-build/session/focal/amd64/rsp-session-focal-{{ PWB_VERSION }}-amd64.tar.gz
    tar xfz rsp-session-focal-{{ PWB_VERSION }}-amd64.tar.gz -C /usr/lib/rstudio-server --strip=1
    rm -f rsp-session-focal-{{ PWB_VERSION }}-amd64.tar.gz

    #!/bin/bash
    # Install Java JDK (optional) 
    apt-get update -y && \
        DEBIAN_FRONTEND=noninteractive apt-get install -y \
	    default-jdk 

    # Install and configure new set of defined R versions
    for R_VERSION in {{ R_VERSION_LIST }}
    do
        curl -O https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-${R_VERSION}_1_amd64.deb && \
        gdebi -n r-${R_VERSION}_1_amd64.deb && \
        rm -f r-${R_VERSION}_1_amd64.deb

        # Reconfigure R for Java (optional) 
        export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
        /opt/R/${R_VERSION}/bin/R CMD javareconf
	echo $JAVA_HOME/lib/server > /etc/ld.so.conf.d/java.conf

        # Need to make sure R is in PATH so that pak can run R as a subprocess

        PATH=/opt/R/${R_VERSION}/bin:$PATH /opt/R/${R_VERSION}/bin/Rscript /run.R
    done
    rm -f /run.R

    # Defining system default version
    if [ ! -z {{ R_VERSION_DEFAULT }} ]; then
        ln -s /opt/R/{{ R_VERSION_DEFAULT }}/bin/R /usr/local/bin
        ln -s /opt/R/{{ R_VERSION_DEFAULT }}/bin/Rscript /usr/local/bin
    fi

    # Installing frequently needed system dependencies 
    # (Cf. https://docs.posit.co/connect/admin/r/dependencies/)
    apt install -y libcairo2-dev libssl-dev make libcurl4-openssl-dev \
            libmysqlclient-dev unixodbc-dev libnode-dev default-jdk libxml2-dev \
            git libfontconfig1-dev libfreetype6-dev libssh2-1-dev zlib1g-dev \
            libglpk-dev libjpeg-dev imagemagick libmagick++-dev gsfonts cmake \
            libpng-dev libtiff-dev python3 libglu1-mesa-dev libgl1-mesa-dev \
            libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev \
            libsodium-dev libicu-dev tcl tk tk-dev tk-table libfribidi-dev \
            libharfbuzz-dev libudunits2-dev

    # Install zeromq as prereq for clustermq (optional) 
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
        libzmq5 

    # Install JAGS as prereq for rjags (optional)
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
        jags

    # Install SLURM
    groupadd -g 401 slurm
    useradd -u 401 -g 401 slurm
    apt-get install -y libmunge-dev

    # Note that the git branches on github do have a slightly different
    # naming scheme - firstly the dots are replaced by dashes and
    # secondly each SLURM version can have more than one release tag
    # Here, we simply append "-1" to use the first git tag of a given
    # SLURM version

    dir=`mktemp -d` && \
        cd $dir && \
        rm -rf slurm && \
        export SLURM_VER={{ SLURM_VERSION }} && git clone --depth 1 -b slurm-${SLURM_VER//./-}-1 https://github.com/SchedMD/slurm.git && \
        cd slurm && \
        ./configure --prefix /usr/local/slurm > /var/log/slurm-configure.log && \
        echo "Compiling SLURM" && \
        make -j 4 > /var/log/slurm-compile.log && \
        echo "Installing SLURM" && \
        make install > /var/log/slurm-install.log && \
        cd / && \
        rm -rf $dir && \
        ln -s /usr/local/slurm/bin/* /usr/local/bin

    #Install Apptainer
    dir=`mktemp -d`
    cd $dir  
    curl -L -O https://github.com/apptainer/apptainer/releases/download/v{{ APPTAINER_VERSION }}/apptainer_{{ APPTAINER_VERSION }}_amd64.deb
    curl -L -O https://github.com/apptainer/apptainer/releases/download/v{{ APPTAINER_VERSION }}/apptainer-suid_{{ APPTAINER_VERSION }}_amd64.deb
    gdebi -n apptainer_{{ APPTAINER_VERSION }}_amd64.deb 
    gdebi -n apptainer-suid_{{ APPTAINER_VERSION }}_amd64.deb
    rm -f apptainer*
    cd 
    rm -rf $dir 

    rm -rf /var/cache/yum/*


#%startscript
#    # The below is saving the necessary environment variables so they can eb inherited into
#    # subsequent singularity calls
#    env | grep -e ^SINGULARITY -e ^SLURM | grep -v NAME | grep -v BIND | sed 's/^/export /' > /tmp/.slurm-$USER-$SLURM_JOBID.env
#    $@

%environment  
    TINI_SUBREAPER=true
    export SLURM_CONF=/opt/slurm/etc/slurm.conf