Dockerfile

# base image
FROM ubuntu:focal

# metadata
LABEL base.image="ubuntu:focal"
LABEL version="1"
LABEL software="GATK"
LABEL software.version="${gatk_version}"
LABEL description="Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size."
LABEL website="https://github.com/broadinstitute/gatk"
LABEL license="https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT"
LABEL maintainer="Maxime Vallée"
LABEL maintainer.email="maxime.vallee@chu-lyon.fr"

RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
  unzip \
  wget \
  git \
  python3.6 \
  default-jre \
  libgomp1 \
  && apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN cd /opt && \
    gatk_version=4.2.6.1 && \
    wget https://github.com/broadinstitute/gatk/releases/download/${gatk_version}/gatk-${gatk_version}.zip && \
    unzip gatk-${gatk_version}.zip && \
    rm gatk-${gatk_version}.zip

ENV PATH="${PATH}:/opt/gatk-${gatk_version}/"