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Dockerfile
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FROM debian:latest
RUN apt-get update && \
apt-get install -y --no-install-recommends \
g++ \
gcc \
gfortran \
libbz2-dev \
libcurl4-openssl-dev \
libgsl-dev \
libgsl2 \
liblzma-dev \
libncurses5-dev \
libpcre3-dev \
libreadline-dev \
libssl-dev \
make \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
RUN apt-get update --fix-missing && \
apt-get install -y wget bzip2 ca-certificates curl git && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
ENV TINI_VERSION v0.16.1
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini
ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 -o /opt/samtools-1.3.1.tar.bz2 && \
tar xvjf /opt/samtools-1.3.1.tar.bz2 -C /opt/ && \
cd /opt/samtools-1.3.1 && \
make && \
make install && \
rm /opt/samtools-1.3.1.tar.bz2
RUN conda install pandas click