zhooshularity/singularity.def at main · LinkageIO/zhooshularity · GitHub

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Bootstrap: library
From: ubuntu:20.04

%setup

%files
    linkage_env.sh /.singularity.d/env/99-zz_custom_env.sh

%post
    # Do some filesystem setup
    export OPTDIR="/opt/linkage"
    mkdir -p ${OPTDIR}/src
    mkdir -p ${OPTDIR}/share
    mkdir -p ${OPTDIR}/bin
    mkdir -p ${OPTDIR}/home

    # add the universe repo
    apt-get install software-properties-common --yes
    add-apt-repository universe

    # update and install essentials
    apt-get update && apt-get upgrade --yes
    apt-get install \
    curl wget sudo bc \
    zsh  vim git tree tmux\
    parallel \
    default-jre \
    unzip less \
    build-essential \
    --yes

    # oh my zsh
    cd $OPTDIR/home
    git clone https://github.com/ohmyzsh/ohmyzsh.git .oh-my-zsh
    cp .oh-my-zsh/templates/zshrc.zsh-template .zshrc

    # Download and install conda
    cd $OPTDIR/src
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    sh Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
    export PATH="$PATH:/opt/conda/bin"

    # Install snakemake
    conda install -c bioconda -c conda-forge snakemake --yes
    conda init zsh

    # Install some python packages
    #pip install ipython matplotlib xlwt pandas numpy xlrd

%environment
    # These are set at container runtime
    export OPTDIR="/opt/linkage"
    export PATH="$PATH:$OPTDIR/bin"
    export PATH="$PATH:/opt/conda/bin"
    export PATH="$PATH:$HOME/.local/bin"
    # Set the locale so the shell wont complain
    export LANG=C.UTF-8
    export LC_ALL=C.UTF-8
    export MPLCONFIGDIR=/tmp/matplotlib/