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Dockerfile
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# Use ubuntu:latest as parent image
FROM ubuntu:16.04
# Set the working directory in container
WORKDIR /home
# Install python, pip, and aws cli
# Need to install sudo first to remove prompts of [Y/n]
RUN apt-get update && apt-get install -y sudo && rm -rf /var/lib/apt/lists/* \
&& sudo apt-get -y update \
&& sudo apt-get -y install \
build-essential \
git \
groff \
libbz2-dev \
zlib1g-dev \
python-dev \
python-pip \
wget \
&& sudo pip install --upgrade pip \
&& sudo pip install --upgrade virtualenv \
&& sudo pip install awscli --upgrade --user \
&& pip install boto3
RUN wget https://github.com/samtools/htslib/releases/download/1.5/htslib-1.5.tar.bz2 \
&& tar -xvjf htslib-1.5.tar.bz2 \
&& rm htslib-1.5.tar.bz2 \
&& cd htslib-1.5 \
&& ./configure --prefix /usr/local/ --disable-lzma \
&& make \
&& make install
ADD . /home
RUN chmod a+x /home/SDK.sh
ENV PATH=$PATH:/home/triodenovo-fix/bin/:/home/