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Dockerfile
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FROM ppc64le/ubuntu:18.04
RUN apt-get update && \
apt-get install -y python && \
apt-get install -y wget \
curl \
bc \
vim \
time \
unzip \
less \
bedtools \
samtools \
openjdk-8-jdk \
tabix \
software-properties-common && \
apt-get -y clean && \
apt-get -y autoclean && \
apt-get -y autoremove
ENV HOME /root
ENV export JAVA_HOME /usr/lib/jvm/java-8-openjdk-ppc64el
ENV JAVA_LIBRARY_PATH /usr/lib/powerpc64le-linux-gnu/jni
CMD ["bash"]
RUN mkdir -p /apps/bin
RUN mkdir -p /gatk
RUN mkdir -p /data
WORKDIR /gatk
ADD gatk-4.1.8.0 /apps/gatk-4.1.8.0
COPY bin /apps/bin
ADD benchmarks /apps/benchmarks
ENV GATK_HOME /apps
ENV PATH $GATK_HOME/bin:$PATH
ENV GATK_LOCAL_JAR $GATK_HOME/gatk-4.1.8.0/libs/gatk-local.jar
ENV GATK_SPARK_JAR $GATK_HOME/gatk-4.1.8.0/libs/gatk-spark.jar
ENV LD_LIBRARY_PATH $GATK_HOME/gatk-4.1.8.0/libs:$LD_LIBRARY_PATH