rakeiora-workflow-public-somatic-2/singularity.def at main · drai-inn/rakeiora-workflow-public-somatic-2 · GitHub

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BootStrap: docker
From: ubuntu:20.04
Stage: 0

%environment
        export DEBIAN_FRONTEND=noninteractive
        export SAMTOOLS_VERSION=1.19
        export BCFTOOLS_VERSION=1.19
        export JAVA_HOME=/usr/lib/jvm/temurin-20-jdk-amd64
        export PATH=$JAVA_HOME/bin:$PATH
        export VCFANNO_VERSION=v0.3.6

%post
        export DEBIAN_FRONTEND=noninteractive
        export SAMTOOLS_VERSION=1.19
        export BCFTOOLS_VERSION=1.19
        export APT_LISTCHANGES_FRONTEND=none
        export VCFANNO_VERSION=v0.3.6

        # Disable privilege dropping for apt
        echo 'APT::Sandbox::User "root";' > /etc/apt/apt.conf.d/90sandbox

        apt-get -qqy update --fix-missing
        apt-get -qqy dist-upgrade
        apt-get -qqy install --no-install-recommends \
                 ca-certificates \
                 libbz2-dev \
                 libcurl4-openssl-dev \
                 liblzma-dev \
                 libncurses5-dev \
                 libssl-dev \
                 autoconf \
                 automake \
                 bzip2 \
                 gcc \
                 g++ \
                 make \
                 wget \
                 git \
                 zlib1g-dev \
                 gnupg \
                 software-properties-common

        # Install vcfanno
        wget https://github.com/brentp/vcfanno/releases/download/${VCFANNO_VERSION}/vcfanno_linux64
        chmod +x ./vcfanno_linux64
        cp vcfanno_linux64 /usr/local/bin/vcfanno

       # Install Java 20
        wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | apt-key add -
        echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
        apt-get -qqy update
        apt-get -qqy install --no-install-recommends temurin-20-jdk

        # Install SAMtools
        wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
        tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2
        cd samtools-${SAMTOOLS_VERSION}
        ./configure --without-curses
        make -s all all-htslib
        make install install-htslib
        cd /
        rm -rf samtools-${SAMTOOLS_VERSION}*

        # Install BCFtools (matching SAMtools version)
        wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
        tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2
        cd bcftools-${BCFTOOLS_VERSION}
        ./configure --without-curses
        make -s
        make install
        cd /
        rm -rf bcftools-${BCFTOOLS_VERSION}*

        # Clone and compile vt
        git clone https://github.com/atks/vt.git
        cd vt
        git submodule update --init --recursive
        make
        # Install vt binary to system path
        cp vt /usr/local/bin/
        cd /
        rm -rf vt

        # Clean up
        apt-get -qqy purge autoconf automake bzip2 gcc g++ make wget git libssl-dev
        apt-get -qqy clean
        apt-get -qqy autoremove
        rm -rf /var/cache/apt/archives/* /var/lib/apt/lists/* /usr/share/man/?? /usr/share/man/??_*
        find /tmp -name "*.tar.*" -delete 2>/dev/null || true
        find /tmp -name "*.log" -delete 2>/dev/null || true

%test
        samtools --help
        bcftools --help
        # Can't run this because it exits with nonzero status, but it works
        # vcfanno