fburic/candia:def

$ singularity pull shub://fburic/candia:def

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda3:4.8.3

%files
    candia_env.yaml
    
%post
    mkdir -p /cephyr
    mkdir -p /local
    mkdir -p /apps
    mkdir -p /usr/share/lmod/lmod
    mkdir -p /var/hasplm
    mkdir -p /var/opt/thinlinc
    mkdir -p /usr/lib64
    touch /usr/lib64/libdlfaker.so
    touch /usr/lib64/libvglfaker.so
    touch /usr/bin/nvidia-smi

    apt-get update && apt-get install -y --no-install-recommends libgomp1 libicu-dev  build-essential libcurl4-openssl-dev libxml2-dev libssl-dev r-base pandoc libz-dev

    /opt/conda/bin/conda env update --name base --file candia_env.yaml --prune

    ######
    # Workaround: Use conda JDK package since Spark looks for older Java 1.8.0 in system dir
    ######
    mkdir -p /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin
    ln -s /opt/conda/bin/java /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin/java

    ######
    # Workaround: C libraries installed by conda as dependencies are a bit ouf date so we use the system ones
    # Ref: https://conda.continuum.narkive.com/nGVLDlYz/r-jupyter-cxxabi-version-not-found
    ######
    mv /opt/conda/lib/libstdc++.so.6 /opt/conda/lib/libstdc++.so.6_conda
    mv /opt/conda/lib/libgomp.so.1 /opt/conda/lib/libgomp.so.1_conda
    ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/conda/lib/libstdc++.so.6
    ln -s /usr/lib/x86_64-linux-gnu/libgomp.so.1 /opt/conda/lib/libgomp.so.1

    # Avoid warnings about locale
    echo 'en_US.UTF-8 UTF-8' >> /etc/locale.gen
    locale-gen && update-locale LANG=en_US.UTF-8


    #####
    # Install R pacakges
    #####
    R -e "install.packages('devtools', dependencies = T)" && R -e "library('devtools'); install_version('tidyverse', version='1.3.0'); install_version('data.table', version='1.12.8')"
    R -e "install.packages(c('feather', 'filesstrings', 'optparse', 'yaml'))"



%environment
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/conda/lib


%runscript
    exec "$@"

Collection

• Name: fburic/candia
• License: Other

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