Dockerfile

ARG SNPEFF_VER="5.1d"
ARG SNPEFF_JAR_VER="5.1"
ARG SNPSIFT_VER="5.1"

FROM ubuntu:focal as app

ARG SNPEFF_VER
ARG SNPEFF_JAR_VER
ARG SNPSIFT_VER

# Metadata
LABEL base.image="ubuntu:focal"
LABEL dockerfile.version="1"
LABEL software="SnpEff & SnpSift"
LABEL snpeff.software.version=$SNPEFF_VER
LABEL snpeff.jarfile.version=$SNPEFF_JAR_VER
LABEL snpsift.software.version=$SNPSIFT_VER
LABEL description.SnpEff="Genetic variant annotation and effect prediction toolbox."
LABEL description.SnpSift="Used after SnpEff annotation to filter and manipulate annotated files."
LABEL website="https://pcingola.github.io/SnpEff"
LABEL license="https://github.com/pcingola/SnpEff/blob/master/LICENSE.md"
LABEL maintainer="Tom Iverson"
LABEL maintainer.email="tiverson@utah.gov"

# Install open using apt 
RUN apt-get update && apt-get install -y software-properties-common &&\
  apt-get update && apt-get install -y \
  openjdk-11-jre \
  ant \
  maven \
  wget && apt-get autoclean && rm -rf /var/lib/apt/lists/*

# Use wget to get the source code for SnpEff and SnpSift from GitHub.
RUN wget https://github.com/pcingola/SnpEff/archive/refs/tags/v${SNPEFF_VER}.tar.gz && \
  tar -xvf v${SNPEFF_VER}.tar.gz && \
  rm v${SNPEFF_VER}.tar.gz && \ 
  wget https://github.com/pcingola/SnpSift/archive/refs/tags/v${SNPSIFT_VER}.tar.gz && \
  tar -xvf v${SNPSIFT_VER}.tar.gz && \
  rm v${SNPSIFT_VER}.tar.gz

# Install dependencies and snpEff/SnpSift executables from the source code using Maven.
RUN cd SnpEff-${SNPEFF_VER}/lib && \
  mvn install:install-file -Dfile=antlr-4.5.1-complete.jar -DgroupId=org.antlr -DartifactId=antlr -Dversion=4.5.1 -Dpackaging=jar && \
  mvn install:install-file -Dfile=biojava3-core-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-core -Dversion=3.0.7 -Dpackaging=jar && \
  mvn install:install-file -Dfile=biojava3-structure-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-structure -Dversion=3.0.7 -Dpackaging=jar && \
  cd ../ && \
  mvn clean compile assembly:single jar:jar && \
  cp target/SnpEff-${SNPEFF_JAR_VER}-jar-with-dependencies.jar /snpEff.jar && \
  mvn install:install-file -Dfile=target/SnpEff-${SNPEFF_JAR_VER}.jar -DgroupId=org.snpeff -DartifactId=SnpEff -Dversion=${SNPEFF_JAR_VER} -Dpackaging=jar -DgeneratePom=true --quiet && \
  cd ../ && \
  cd SnpSift-${SNPSIFT_VER} && \
  mvn clean compile assembly:single jar:jar && \
  cp target/SnpSift-${SNPSIFT_VER}-jar-with-dependencies.jar /SnpSift.jar && \
  mvn install:install-file -Dfile=target/SnpSift-${SNPSIFT_VER}.jar -DgroupId=org.snpsift -DartifactId=SnpSift -Dversion=${SNPSIFT_VER} -Dpackaging=jar -DgeneratePom=true --quiet && \
  cd ../ && \
  cd SnpEff-${SNPEFF_VER}

# Modify java executables and set environment variable $PATH
RUN mv SnpEff-${SNPEFF_VER} snpEff && \
  mv snpEff.jar snpEff && \
  mv SnpSift.jar snpEff && \
  chmod +x /snpEff/snpEff.jar && \
  echo "#!/bin/bash" >> /snpEff/snpeff && \
  chmod +x /snpEff/SnpSift.jar && \
  echo "#!/bin/bash" >> /snpEff/snpsift && \
  echo "exec java -jar /snpEff/snpEff.jar """"$""@"""" " >> /snpEff/snpeff && \
  chmod +x /snpEff/snpeff && \
  echo "exec java -jar /snpEff/SnpSift.jar """"$""@"""" " >> /snpEff/snpsift && \
  chmod +x /snpEff/snpsift
ENV PATH="${PATH}:/snpEff" 

# Set working directory
RUN mkdir /data
WORKDIR /data

# Run test of annotation
FROM app as test

COPY test_snpeff_snpsift.sh .
RUN bash test_snpeff_snpsift.sh