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FROM ubuntu:xenial | ||
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SHELL ["/bin/bash", "-c"] | ||
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ENV LC_ALL C.UTF-8 | ||
ENV LANG C.UTF-8 | ||
ENV PATH /opt/conda/bin:${PATH} | ||
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COPY . /source/mutacc | ||
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RUN apt-get update --fix-missing && apt-get install -y \ | ||
build-essential \ | ||
coreutils \ | ||
dialog \ | ||
git \ | ||
language-pack-en-base \ | ||
libbz2-dev \ | ||
libcurl4-openssl-dev \ | ||
liblzma-dev \ | ||
libncurses5-dev \ | ||
libncursesw5-dev \ | ||
libreadline-dev \ | ||
libssl-dev \ | ||
unzip \ | ||
wget \ | ||
zlib1g-dev && apt-get clean | ||
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RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh -O ~/miniconda.sh && \ | ||
/bin/bash ~/miniconda.sh -b -p /opt/conda && \ | ||
rm ~/miniconda.sh && \ | ||
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ | ||
source /opt/conda/etc/profile.d/conda.sh && \ | ||
conda clean -tipsy | ||
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RUN conda config --add channels defaults && \ | ||
conda config --add channels conda-forge && \ | ||
conda config --add channels bioconda && \ | ||
conda install --yes python=3.6 cython=0.29 numpy=1.17 picard=2.18 seqkit=0.11 && \ | ||
conda clean -tipsy | ||
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RUN pip install source/mutacc |