STITCH/dockerfile at main · dimi-lab/STITCH · GitHub

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# -----------------------------
# Builder stage
# -----------------------------
FROM rocker/r-ver:4.4.1 AS builder

WORKDIR /project

# -----------------------------
# Environment variables
# -----------------------------
ENV DEBIAN_FRONTEND=noninteractive
ENV MAKEFLAGS="-j2"
ENV CONDA_DIR=/opt/conda
ENV PATH=$CONDA_DIR/bin:$PATH
ENV RENV_PATHS_CACHE=/project/renv/cache

# -----------------------------
# System dependencies (R + Python)
# -----------------------------
RUN apt-get update && apt-get install -y \
    wget curl git \
    libcurl4-openssl-dev libssl-dev libxml2-dev \
    libpng-dev libhdf5-dev libmagick++-dev \
    libblas-dev liblapack-dev gfortran \
    pandoc libzip-dev libfreetype6-dev libtiff5-dev \
    build-essential libgmp-dev libharfbuzz-dev libfribidi-dev \
    libfontconfig1-dev pkg-config libgsl-dev libfftw3-dev\
    && apt-get clean && rm -rf /var/lib/apt/lists/*

# -----------------------------
# Install renv
# -----------------------------
RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')"

# -----------------------------
# Copy renv project files
# -----------------------------
RUN mkdir -p /project/renv
COPY renv.lock /project/renv.lock
COPY .Rprofile /project/.Rprofile
COPY renv/activate.R /project/renv/activate.R
COPY renv/settings.json /project/renv/settings.json

# -----------------------------
# Restore R packages (cached layers)
# -----------------------------
RUN R -e "renv::restore()"

# -----------------------------
# Install Miniconda
# -----------------------------
ENV CONDA_VERSION=25.9.1-3
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py39_${CONDA_VERSION}-Linux-x86_64.sh -O /tmp/miniconda.sh \
    && /bin/bash /tmp/miniconda.sh -b -p $CONDA_DIR \
    && rm /tmp/miniconda.sh \
    && $CONDA_DIR/bin/conda clean --all --yes \
    && ln -s $CONDA_DIR/bin/conda /usr/local/bin/conda

# Accept TOS
RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r

# -----------------------------
# Copy Conda environment and create env
# -----------------------------
COPY environment.yml /project/environment.yml
RUN conda env create -f /project/environment.yml \
    && conda clean --all --yes

# -----------------------------
# Copy source code
# -----------------------------
RUN git clone https://github.com/dimi-lab/STITCH.git /project/STITCH_src \
    && cd /project/STITCH_src \
    && cp -r assets/ docs/ scripts/ /project/ \
    && rm -rf /project/STITCH_src

# At this point, builder stage has:
# - /project/renv/cache
# - /opt/conda/envs/stitch_env
# - /project source code

# -----------------------------
# Final stage
# -----------------------------
FROM rocker/r-ver:4.4.1

WORKDIR /project

RUN apt-get update && apt-get install -y \
    libcurl4-openssl-dev libssl-dev libxml2-dev \
    libpng-dev libhdf5-dev libmagick++-dev \
    libblas-dev liblapack-dev \
    pandoc libzip-dev libfreetype6-dev libtiff5-dev \
    libgmp-dev libharfbuzz-dev libfribidi-dev \
    libfontconfig1-dev libgsl-dev libfftw3-dev\
    && apt-get clean && rm -rf /var/lib/apt/lists/*

RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')"

# -----------------------------
# Copy only what we need from builder
# -----------------------------
COPY --from=builder /project /project
COPY --from=builder /opt/conda/ /opt/conda/
RUN rm -rf /opt/conda/pkgs/*
RUN ln -s /opt/conda/bin/conda /usr/local/bin/conda || true

ENV PATH=/opt/conda/envs/stitch_env/bin:/opt/conda/bin:$PATH
ENV RENV_PATHS_CACHE=/project/renv/cache
ENV RETICULATE_PYTHON=/opt/conda/envs/stitch_env/bin/python

WORKDIR /project
CMD ["/bin/bash"]