Dockerfile

FROM maven:3-openjdk-11

ENV GN_HOME=/genome-nexus-annotation-pipeline
COPY . $GN_HOME
WORKDIR $GN_HOME

COPY annotationPipeline/src/main/resources/log4j.properties.EXAMPLE $GN_HOME/annotationPipeline/src/main/resources/log4j.properties
# set log4j file in properties
RUN sed -i "s|log4j\.appender\.a\.File.*|log4j.appender.a.File = $GN_HOME/logs/genome-nexus-annotation-pipeline.log|" $GN_HOME/annotationPipeline/src/main/resources/log4j.properties

ARG mvnprofiles=''
RUN mvn -DskipTests clean install $mvnprofiles


FROM openjdk:11-slim

ENV GN_HOME=/genome-nexus-annotation-pipeline

COPY --from=0 $GN_HOME/annotationPipeline/target/annotationPipeline-*.jar $GN_HOME/annotationPipeline/target/annotationPipeline.jar

COPY annotationPipeline/src/main/resources/application.properties.EXAMPLE $GN_HOME/annotationPipeline/src/main/resources/application.properties

RUN apt-get update && apt-get install procps -y