container.def

Bootstrap: library
From: ubuntu:22.04

%post
    TZ=Etc/UTC && \
        ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
        echo $TZ > /etc/timezone

    apt-get -y update

    apt-get install --assume-yes wget bzip2

    wget https://downloads.python.org/pypy/pypy3.10-v7.3.15-linux64.tar.bz2
    tar -xjf pypy3.10-v7.3.15-linux64.tar.bz2
    rm pypy3.10-v7.3.15-linux64.tar.bz2
    mv pypy3.10-v7.3.15-linux64 /opt/pypy3
    /opt/pypy3/bin/pypy3 -m ensurepip
    /opt/pypy3/bin/pypy3 -m pip install cigar

    apt-get install --assume-yes software-properties-common
    add-apt-repository universe
    apt-get update
    apt-get install --assume-yes pigz python3-pip git build-essential zlib1g-dev libjellyfish-2.0-dev pkg-config cmake r-base-core gawk autoconf rustc cargo

    apt-get -y install \
    libssl-dev \
    libxml2-dev \
    libcurl4-openssl-dev \
    curl libgomp1


    git clone https://github.com/cgroza/panmethyl
    cd panmethyl/tagtobed
    cargo build --release 
    cp target/release/tagtobed /usr/local/bin
    cd ${HOME}
    rm -rf panmethyl

    git clone --recursive https://github.com/samtools/htslib.git
    cd htslib
    autoreconf -i
    ./configure
    make
    make install
    cd ${HOME}

    git clone https://github.com/samtools/samtools.git
    cd samtools
    autoheader
    autoconf -Wno-syntax
    ./configure --without-curses
    make
    make install
    cd ${HOME}
    rm -rf samtools

    cd ${HOME}
    rm -rf htslib
    rm -rf bcftools

    git clone https://github.com/lh3/minimap2
    cd minimap2
    make
    cp minimap2 /usr/local/bin
    cd $HOME
    rm -rf minimap2

    git clone https://github.com/lh3/minigraph
    cd minigraph
    make
    cp minigraph /usr/local/bin
    cd ${HOME}
    rm -r minigraph

    git clone https://github.com/lh3/gfatools
    cd gfatools
    make
    cp gfatools /usr/local/bin
    cd ${HOME}
    rm -r gfatools


    # R --slave -e 'install.packages(c("XML", "dplyr", "stringr", "tidyr", "readr", "vcfR", "optparse"), repos="https://cloud.r-project.org/")'

    cd $HOME

    wget -O /usr/local/bin/vg https://github.com/vgteam/vg/releases/download/v1.45.0/vg
    chmod +x /usr/local/bin/vg

    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    bash ~/miniconda.sh -b -p $HOME/miniconda
    rm -f ~/miniconda.sh
    ${HOME}/miniconda/bin/conda install -y -c bioconda graphaligner
    cp ${HOME}/miniconda/bin/GraphAligner /usr/local/bin/
    rm -rf ~/miniconda


    apt-get remove --assume-yes git software-properties-common cmake make pkg-config build-essential autoconf wget rustc cargo
    apt-get autoremove --assume-yes
    apt-get clean --assume-yes


%environment
    export LC_ALL=C
    export LANG=C
    export PYTHONIOENCODING=utf8
    export PATH=/opt/pypy3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin