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Dockerfile
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FROM dceoy/jupyter:latest AS builder
COPY --from=dceoy/samtools:latest /usr/local/src/samtools /usr/local/src/samtools
COPY --from=dceoy/bcftools:latest /usr/local/src/bcftools /usr/local/src/bcftools
ADD . /tmp/pdbio
RUN set -e \
&& apt-get -y update \
&& apt-get -y dist-upgrade \
&& apt-get -y install --no-install-recommends --no-install-suggests \
libbz2-dev libcurl4-gnutls-dev libncurses5-dev libgsl-dev libperl-dev \
liblzma-dev libssl-dev libz-dev make \
&& apt-get -y autoremove \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN set -e \
&& cd /usr/local/src/samtools/htslib-* \
&& make clean \
&& ./configure \
&& make \
&& make install \
&& cd /usr/local/src/samtools \
&& make clean \
&& ./configure \
&& make \
&& make install \
&& cd /usr/local/src/bcftools/htslib-* \
&& make clean \
&& ./configure \
&& make \
&& cd /usr/local/src/bcftools \
&& make clean \
&& ./configure --enable-libgsl --enable-perl-filters \
&& make \
&& make install
RUN set -e \
&& pip install -U --no-cache-dir pip /tmp/pdbio \
&& rm -rf /tmp/pdbio
FROM dceoy/jupyter:latest
COPY --from=builder /usr/local /usr/local
RUN set -e \
&& apt-get -y update \
&& apt-get -y dist-upgrade \
&& apt-get -y install --no-install-recommends --no-install-suggests \
libcurl4-gnutls-dev libgsl-dev libncurses5 \
&& apt-get -y autoremove \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
ENTRYPOINT ["jupyter"]