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GATK4 Dockerfile (4.0.4.0)
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# Using OpenJDK 8 | |
FROM broadinstitute/gatk:gatkbase-1.2.3 | |
ARG DRELEASE | |
ADD . /gatk | |
WORKDIR /gatk | |
RUN /gatk/gradlew clean compileTestJava sparkJar localJar createPythonPackageArchive -Drelease=$DRELEASE | |
WORKDIR /root | |
# Make sure we can see a help message | |
RUN ln -sFv /gatk/build/libs/gatk.jar | |
RUN java -jar gatk.jar -h | |
#Setup test data | |
WORKDIR /gatk | |
# Create link to where test data is expected | |
RUN ln -s /testdata src/test/resources | |
# Create a simple unit test runner | |
ENV CI true | |
RUN echo "source activate gatk" > /root/run_unit_tests.sh && \ | |
echo "cd /gatk/ && ./gradlew jacocoTestReport" >> /root/run_unit_tests.sh | |
WORKDIR /root | |
RUN cp -r /root/run_unit_tests.sh /gatk | |
RUN cp -r gatk.jar /gatk | |
RUN cp -r install_R_packages.R /gatk | |
# Start GATK Python environment | |
ENV DOWNLOAD_DIR /downloads | |
ENV CONDA_URL https://repo.continuum.io/miniconda/Miniconda3-4.3.30-Linux-x86_64.sh | |
ENV CONDA_MD5 = "0b80a152332a4ce5250f3c09589c7a81" | |
ENV CONDA_PATH /opt/miniconda | |
RUN mkdir $DOWNLOAD_DIR && \ | |
wget -nv -O $DOWNLOAD_DIR/miniconda.sh $CONDA_URL && \ | |
test "`md5sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS=' ' '{print $1}'` = $CONDA_MD5" && \ | |
bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \ | |
rm $DOWNLOAD_DIR/miniconda.sh | |
ENV PATH $CONDA_PATH/envs/gatk/bin:$CONDA_PATH/bin:$PATH | |
WORKDIR /gatk | |
RUN conda env create -n gatk -f /gatk/scripts/gatkcondaenv.yml && \ | |
echo "source activate gatk" >> /gatk/gatkenv.rc | |
CMD ["bash", "--init-file", "/gatk/gatkenv.rc"] | |
# End GATK Python environment | |
WORKDIR /gatk | |
ENV PATH /gatk:$PATH |
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