Dockerfile

ARG VERSION=0.3.2-morphic
FROM debian:bookworm-slim as chromap_builder
#put builder tools in
RUN apt-get update && apt-get install -y \
    build-essential \
    curl \
    zlib1g-dev \
    git \
    autoconf \
    automake \
    libtool \
    libcurl4-openssl-dev \
    libssl-dev \
    libbz2-dev \
    liblzma-dev \
    libdeflate-dev \
    && rm -rf /var/lib/apt/lists/*


RUN git clone --recursive https://github.com/morphic-bio/chromap.git /chromap
WORKDIR /chromap
RUN git fetch origin && git checkout 537e5fd && git submodule update --init --recursive
# Build htslib first (required dependency)
WORKDIR /chromap/third_party/htslib
# Generate missing version.h for htscodecs before building
RUN if [ -d htscodecs/htscodecs ] && [ ! -f htscodecs/htscodecs/version.h ]; then \
      ver="unknown"; \
      if git -C htscodecs describe --match 'v[0-9].[0-9]*' --dirty >/dev/null 2>&1; then \
        ver=$(git -C htscodecs describe --match 'v[0-9].[0-9]*' --dirty); \
        ver=${ver#v}; \
      fi; \
      echo "#define HTSCODECS_VERSION_TEXT \"${ver}\"" > htscodecs/htscodecs/version.h; \
    fi
# Configure and build htslib (disable optional features we don't need)
RUN autoreconf -i && \
    ./configure --disable-bz2 --disable-lzma --disable-libdeflate --without-libcurl && \
    make clean && make -j 4
# Build chromap
WORKDIR /chromap
RUN make clean && make -j 8

#Python3 will be the base image and we will install macs2 and macs3 bedtools and samtools
FROM python:3.9-slim

RUN apt-get update && apt-get install -y zlib1g-dev bedtools samtools tabix curl \
    && rm -rf /var/lib/apt/lists/*
RUN curl -L -o /usr/local/bin/bedGraphToBigWig https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig \
    && chmod +x /usr/local/bin/bedGraphToBigWig


RUN pip install numpy pyBigWig pyfaidx pandas termcolor modisco-lite modisco==0.5.16.4
RUN apt-get update && apt-get install -y gcc && \
    pip install macs2 &&  pip install macs3 && \
    apt-get remove -y gcc && rm -rf /var/lib/apt/lists/*
#install gawk
RUN apt-get update && apt-get install -y gawk && \
    rm -rf /var/lib/apt/lists/*
#copy the chromap binary and htslib libraries from the chromap_builder image
COPY --from=chromap_builder /chromap*/chromap /usr/local/bin/chromap
COPY --from=chromap_builder /chromap/third_party/htslib/libhts.so* /usr/local/lib/
RUN ldconfig