Dockerfile

# base image
FROM ubuntu:focal

# metadata
LABEL base.image="ubuntu:focal"
LABEL version="1"
LABEL software="snpEff"
LABEL software.version="5.1"
LABEL description=" Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). SnpSift annotates genomic variants using databases, filters, and manipulates genomic annotated variants. Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants for your experiment."
LABEL website="http://pcingola.github.io/SnpEff/"
LABEL license="https://github.com/pcingola/SnpEff/blob/master/LICENSE.md"
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 \
  default-jre \
  && apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN cd /opt && \
  wget --no-check-certificate --tries=0 -P /opt https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip && \
  unzip /opt/snpEff_latest_core.zip -d /opt && \
  rm -rf /opt/snpEff_latest_core.zip /opt/clinEff /opt/snpEff/examples /opt/snpEff/galaxy && \
  ln /opt/snpEff/snpEff.jar /opt/snpEff.jar && \
  ln /opt/snpEff/SnpSift.jar /opt/SnpSift.jar

ENV PATH="${PATH}:/opt/"