CODECSuite.Dockerfile

FROM debian:bookworm-20250113-slim AS base

ENV LANG=C.UTF-8

RUN apt-get update \
    && apt-get install -y --no-install-recommends \
        build-essential \
        cmake \
        git \
        gnupg \
        openjdk-17-jdk-headless \
        procps \
        ssh \
    && rm -rf /var/lib/apt/lists/*

FROM base AS codec

RUN apt-get update \
    && apt-get install -y --no-install-recommends \
        libbz2-dev \
        liblzma-dev \
        libz-dev \
    && rm -rf /var/lib/apt/lists/*

RUN git clone --recursive \
        https://github.com/broadinstitute/CODECsuite.git \
        /opt/CODEC

ARG CODEC_VERSION=fa0a843933ebba8726b37d449ae557c828717aaa

RUN cd /opt/CODEC \
    && git fetch origin \
    && git checkout ${CODEC_VERSION}

COPY <<"EOF" /opt/CODEC/fermi-lite.patch
@@ -33,1 +33,1 @@
-const uint8_t rle_auxtab[8];
+extern const uint8_t rle_auxtab[8];
EOF

RUN patch /opt/CODEC/bbcpputil/third_party/SeqLib/fermi-lite/rle.h \
    < /opt/CODEC/fermi-lite.patch

RUN mkdir /opt/CODEC/build \
    && cd /opt/CODEC/build/ \
    && cmake ../ \
    && make

FROM base

COPY --from=codec /opt/CODEC/build/codec /bin/codec