Dockerfile.kegalign

# Reminder: if updating this image, also update it in build-tools/makeGpuDockerRelease
FROM nvidia/cuda:11.7.1-devel-ubuntu22.04 as builder

# Prevent dpkg from trying to ask any questions, ever
ENV DEBIAN_FRONTEND noninteractive

# system dependencies are installed by ./installUbuntu.sh below, but we need sudo first
RUN apt-get -qq -y update && \
    apt-get -qq -y upgrade && \
    apt-get -qq -y install \
    git build-essential wget curl jq dos2unix

# Use the commit from the file
COPY build-tools/KegAlign.commit /

# clone KegAlign
RUN git clone https://github.com/galaxyproject/KegAlign.git && cd KegAlign && git checkout $(cat /KegAlign.commit) && git submodule update --init --recursive

# make the conda environment
RUN cd /KegAlign && \
    dos2unix ./scripts/*.bash ./scripts/*.py ./scripts/run_kegalign && \
    ./scripts/make-conda-env.bash -dev

# build KegAlign
RUN cd /KegAlign && \
    mkdir build && \
    bash -c "source ./conda-env-dev.bash && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && make -j $(nproc)"

# Create a thinner final Docker image with only runtime dependencies
FROM nvidia/cuda:11.7.1-runtime-ubuntu22.04

# Install runtime dependencies
RUN apt-get -qq -y update && \
    apt-get -qq -y upgrade  && \
    apt-get -qq -y install mbuffer

# copy kegalign runtime essentials (for historic reasons, cactus is in /home so we put kegalign there too)
RUN mkdir /home/KegAlign /home/KegAlign/bin
COPY --from=builder /KegAlign/build/kegalign /home/KegAlign/bin/
COPY --from=builder /KegAlign/scripts /home/KegAlign/scripts
COPY --from=builder /KegAlign/.conda/miniforge3/envs/kegalign-dev/lib /home/KegAlign/lib

# add the library path
ENV LD_LIBRARY_PATH="/home/KegAlign/lib:${LD_LIBRARY_PATH}"

# add the kegalign path
ENV PATH="/home/KegAlign/bin:/home/KegAlign/scripts:${PATH}"

# remember that commit
COPY --from=builder /KegAlign.commit /

# UCSC convention is to work in /data
RUN mkdir -p /data
WORKDIR /data