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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 python-pip python-dev build-essential \
&& sudo apt-get install -y groff \
&& sudo pip install --upgrade pip \
&& sudo pip install --upgrade virtualenv \
&& sudo pip install awscli --upgrade --user \
&& sudo apt-get install git -y \
&& pip install boto3 \
&& pip install fasteners
RUN sudo apt-get install default-jre -y \
&& sudo apt-get install default-jdk -y \
&& git clone https://github.com/broadinstitute/picard.git \
&& cd picard/ \
&& ./gradlew shadowJar
ADD . /home
RUN chmod a+x /home/SDK.sh