Add Dockerfile installing p4 and a variery of tools

BAMBI_VERSION="0.17.1"
BIOBAMBAM2_VERSION="2.0.185-release-20221211202123"
BWA_VERSION="0.7.18"
DEFLATE_VERSION="1.20"
HTSLIB_VERSION="1.20"
LIBMAUS2_VERSION="2.0.813-release-20221210220409"
NPG_SEQ_COMMON_VERSION="51.1"
SAMTOOLS_VERSION="1.20"
TEEPOT_VERSION="1.2.0"

.dockerignore

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+.DS_Store
+*~
+*.iml
+.idea/

Dockerfile

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+ARG BASE_IMAGE=ubuntu:22.04
+
+ARG BAMBI_VERSION="0.17.1"
+ARG BIOBAMBAM2_VERSION="2.0.185-release-20221211202123"
+ARG BWA_VERSION="0.7.18"
+ARG DEFLATE_VERSION="1.20"
+ARG HTSLIB_VERSION="1.20"
+ARG LIBMAUS2_VERSION="2.0.813-release-20221210220409"
+ARG NPG_SEQ_COMMON_VERSION="51.1"
+ARG SAMTOOLS_VERSION="1.20"
+ARG TEEPOT_VERSION="1.2.0"
+
+FROM $BASE_IMAGE as build
+
+WORKDIR /tmp
+
+RUN DEBIAN_FRONTEND=noninteractive apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    apt-utils \
+    ca-certificates \
+    curl \
+    dirmngr \
+    gpg \
+    gpg-agent \
+    lsb-release \
+    locales && \
+    locale-gen en_GB en_GB.UTF-8 && \
+    localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8
+
+ENV LANG=en_GB.UTF-8 \
+    LANGUAGE=en_GB \
+    LC_ALL=en_GB.UTF-8
+
+# Build tools
+RUN apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    autoconf \
+    automake \
+    build-essential \
+    cmake \
+    gcc \
+    git \
+    libtool \
+    make \
+    perl \
+    pkg-config \
+    unattended-upgrades
+
+# OS build dependencies
+RUN apt-get install -q -y --no-install-recommends \
+    cpanminus \
+    libboost-dev \
+    libbz2-dev \
+    libcurl4-gnutls-dev  \
+    liblzma-dev \
+    libssl-dev \
+    libxml2-dev \
+    zlib1g-dev
+
+RUN unattended-upgrade -v
+
+ARG DEFLATE_VERSION
+RUN curl -sSL -O https://github.com/ebiggers/libdeflate/releases/download/v${DEFLATE_VERSION}/libdeflate-${DEFLATE_VERSION}.tar.gz && \
+    tar xzf libdeflate-${DEFLATE_VERSION}.tar.gz && \
+    cd libdeflate-${DEFLATE_VERSION} && \
+    cmake -DCMAKE_BUILD_TYPE=Release -S . -B ./build && \
+    cmake --build ./build && \
+    cd ./build && \
+    make -j $(nproc) install && \
+    ldconfig
+
+ARG LIBMAUS2_VERSION
+RUN curl -sSL -O "https://gitlab.com/german.tischler/libmaus2/-/archive/${LIBMAUS2_VERSION}/libmaus2-${LIBMAUS2_VERSION}.tar.bz2" && \
+    tar xfj libmaus2-${LIBMAUS2_VERSION}.tar.bz2 && \
+    cd libmaus2-${LIBMAUS2_VERSION} && \
+    ./configure --prefix=/usr/local && \
+    make -j $(nproc) install && \
+    ldconfig
+
+ARG BIOBAMBAM2_VERSION
+RUN curl -sSL -O "https://gitlab.com/german.tischler/biobambam2/-/archive/${BIOBAMBAM2_VERSION}/biobambam2-${BIOBAMBAM2_VERSION}.tar.bz2" && \
+    tar xfj biobambam2-${BIOBAMBAM2_VERSION}.tar.bz2 && \
+    cd biobambam2-${BIOBAMBAM2_VERSION} && \
+    ./configure && \
+    make -j $(nproc) install
+
+ARG TEEPOT_VERSION
+RUN curl -sSL -O "https://github.com/wtsi-npg/teepot/releases/download/${TEEPOT_VERSION}/teepot-${TEEPOT_VERSION}.tar.gz" && \
+    tar xzf teepot-${TEEPOT_VERSION}.tar.gz && \
+    cd teepot-${TEEPOT_VERSION} && \
+    ./configure && \
+    make -j $(nproc) install
+
+ARG HTSLIB_VERSION
+RUN curl -sSL -O "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" && \
+    tar xfj htslib-${HTSLIB_VERSION}.tar.bz2 && \
+    cd htslib-${HTSLIB_VERSION} && \
+    ./configure --with-libdeflate --enable-libcurl --enable-s3 && \
+    make -j $(nproc) install && \
+    ldconfig
+
+ARG SAMTOOLS_VERSION
+RUN curl -sSL -O "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
+    tar xfj samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VERSION} && \
+    ./configure --with-htslib=system --without-curses && \
+    make -j $(nproc) install
+
+ARG BWA_VERSION
+RUN curl -sSL -O "https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VERSION}.tar.gz" && \
+    tar xzf v${BWA_VERSION}.tar.gz && \
+    cd bwa-${BWA_VERSION} && \
+    make -j $(nproc) && \
+    cp ./bwa /usr/local/bin/ && \
+    chmod +x /usr/local/bin/bwa
+
+ARG BAMBI_VERSION
+RUN git clone --single-branch --branch="$BAMBI_VERSION" --depth=1 "https://github.com/wtsi-npg/bambi.git" && \
+    cd bambi && \
+    autoreconf -fi && \
+    ./configure && \
+    make -j $(nproc) install
+
+ARG NPG_SEQ_COMMON_VERSION
+RUN git clone --single-branch --branch="$NPG_SEQ_COMMON_VERSION" --depth=1 "https://github.com/wtsi-npg/npg_seq_common.git" && \
+    cd npg_seq_common && \
+    cp ./bin/seqchksum_merge.pl /usr/local/bin/ && \
+    chmod +x /usr/local/bin/seqchksum_merge.pl
+
+RUN cpanm --notest --local-lib /usr/local/lib Module::Build
+
+COPY . ./p4
+
+RUN cd p4 && \
+    cpanm --notest --local-lib /usr/local/lib --installdeps . && \
+    cpanm --notest --local-lib /usr/local/lib .
+
+
+FROM $BASE_IMAGE
+
+RUN DEBIAN_FRONTEND=noninteractive apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    apt-utils \
+    ca-certificates \
+    lsb-release \
+    unattended-upgrades \
+    locales && \
+    locale-gen en_GB en_GB.UTF-8 && \
+    localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8
+
+ENV LANG=en_GB.UTF-8 \
+    LANGUAGE=en_GB \
+    LC_ALL=en_GB.UTF-8
+
+RUN apt-get install -q -y --no-install-recommends \
+        libboost-atomic1.74.0 \
+        libbz2-1.0 \
+        libcurl4 \
+        liblzma5 \
+        libssl3 \
+        libxml2 \
+        zlib1g \
+        perl && \
+        unattended-upgrade -v && \
+        apt-get remove -q -y unattended-upgrades && \
+        apt-get autoremove -q -y && \
+        apt-get clean -q -y && \
+        rm -rf /var/lib/apt/lists/*
+
+COPY --from=build /usr/local /usr/local
+
+RUN ldconfig
+
+ARG USER=p4user
+ARG UID=1000
+ARG GID=$UID
+
+RUN groupadd --gid $GID $USER && \
+    useradd --uid $UID --gid $GID --shell /bin/bash --create-home $USER
+
+USER $USER
+
+ENTRYPOINT []
+
+CMD ["/bin/bash"]