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ARG PYTHON_VERSION=slim
FROM python:${PYTHON_VERSION}
WORKDIR /workspace
RUN apt-get update && apt-get install --no-install-recommends -y autoconf automake gcc libcurl4-openssl-dev \
make git libc6-dev zlib1g-dev libssl-dev liblzma-dev libbz2-dev libdeflate-dev && \
rm -rf /var/lib/apt/lists/*
COPY . .
RUN pip install -r requirements.txt && pip install pytest pytest-cov
# build cyvcf2
RUN CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate" \
CYTHONIZE=1 python setup.py build_ext -i
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