Dockerfile.python

# ---- Build Golang Binaries ----
FROM golang:1.21.4 AS go-builder

# Set the environment variable for Go binaries. This makes sure the binaries are saved to a defined path.
ENV GOBIN=/app/bin

# Install the specific versions of the Go programs
RUN go install github.com/bystrogenomics/bystro-vcf@2.2.3;

# Use Ubuntu as the base image to match the GitHub Actions environment
FROM python:3.11.8-bookworm

# Copy the compiled Go binaries from the builder stage
COPY --from=go-builder /app/bin/ /app/bin/

# Add app/bin to PATH
ENV PATH="/app/bin:${PATH}"

# # Install common dependencies and utilities
RUN apt-get update && apt-get install -y --no-install-recommends \
    build-essential \
    git \
    wget curl\
    openssl libcurl4-openssl-dev libssl-dev \
    tar lz4 pigz tabix unzip \
    patch \
    awscli \
    unzip \
    libssl-dev \
    pkg-config \ 
    && curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y \
    && . $HOME/.cargo/env

# Make sure Cargo is in the PATH
ENV PATH="/root/.cargo/bin:${PATH}"
ENV PATH="/usr/local/go/bin:${PATH}"

# Set up the workspace
WORKDIR /workspace

COPY ./python ./python
COPY ./config ./config

# Install Python and dependencies
RUN pip install --upgrade pip && pip install python/ -r python/requirements-dev.txt

COPY ./Makefile ./

RUN make install-python

# Run pytest before installation
RUN pytest python/ --maxfail=1 --disable-warnings


ENTRYPOINT ["bystro-api"]

CMD ["--help"]