1# stage 1 for constructing the GATK zip 2FROM broadinstitute/gatk:gatkbase-2.3.0 AS gradleBuild 3LABEL stage=gatkIntermediateBuildImage 4ARG RELEASE=false 5 6RUN ls . 7ADD . /gatk 8WORKDIR /gatk 9 10RUN add-apt-repository universe && apt update 11RUN apt-get --assume-yes install git-lfs 12RUN git lfs install 13 14RUN git lfs pull 15 16RUN export GRADLE_OPTS="-Xmx4048m -Dorg.gradle.daemon=false" && /gatk/gradlew clean collectBundleIntoDir shadowTestClassJar shadowTestJar -Drelease=$RELEASE 17RUN cp -r $( find /gatk/build -name "*bundle-files-collected" )/ /gatk/unzippedJar/ 18RUN unzip -o -j $( find /gatk/unzippedJar -name "gatkPython*.zip" ) -d /gatk/unzippedJar/scripts 19 20# Using OpenJDK 8 21FROM broadinstitute/gatk:gatkbase-2.3.0 22 23WORKDIR /gatk 24 25# Location of the unzipped gatk bundle files 26COPY --from=gradleBuild /gatk/unzippedJar . 27 28#Setup linked jars that may be needed for running gatk 29RUN ln -s $( find /gatk -name "gatk*local.jar" ) gatk.jar 30RUN ln -s $( find /gatk -name "gatk*local.jar" ) /root/gatk.jar 31RUN ln -s $( find /gatk -name "gatk*spark.jar" ) gatk-spark.jar 32 33WORKDIR /root 34 35 # Make sure we can see a help message 36RUN java -jar gatk.jar -h 37RUN mkdir /gatkCloneMountPoint 38RUN mkdir /jars 39RUN mkdir .gradle 40 41WORKDIR /gatk 42 43# Create a simple unit test runner 44ENV CI true 45RUN echo "source activate gatk" > /root/run_unit_tests.sh && \ 46 echo "export GATK_DOCKER_CONTAINER=true" >> /root/run_unit_tests.sh && \ 47 echo "export TEST_JAR=\$( find /jars -name \"gatk*test.jar\" )" >> /root/run_unit_tests.sh && \ 48 echo "export TEST_DEPENDENCY_JAR=\$( find /jars -name \"gatk*testDependencies.jar\" )" >> /root/run_unit_tests.sh && \ 49 echo "export GATK_JAR=$( find /gatk -name "gatk*local.jar" )" >> /root/run_unit_tests.sh && \ 50 echo "export GATK_LAUNCH_SCRIPT=/gatk/gatk" >> /root/run_unit_tests.sh && \ 51 echo "mkdir /gatk/srcdir" >> /root/run_unit_tests.sh && \ 52 echo "cp -rp /gatkCloneMountPoint/src/main/java/* /gatk/srcdir" >> /root/run_unit_tests.sh && \ 53 echo "export SOURCE_DIR=/gatk/srcdir" >> /root/run_unit_tests.sh && \ 54 echo "export GRADLE_OPTS=\"-Xmx1024m -Dorg.gradle.daemon=false\"" /root/run_unit_tests.sh && \ 55 echo "export CP_DIR=/gatk/testClasses" /root/run_unit_tests.sh && \ 56 echo "ln -s /gatkCloneMountPoint/src/ /gatkCloneMountPoint/scripts/docker/src" >> /root/run_unit_tests.sh && \ 57 echo "ln -s /gatkCloneMountPoint/build/ /gatkCloneMountPoint/scripts/docker/build" >> /root/run_unit_tests.sh && \ 58 echo "cd /gatk/ && /gatkCloneMountPoint/gradlew -b /gatkCloneMountPoint/dockertest.gradle testOnPackagedReleaseJar jacocoTestReportOnPackagedReleaseJar -a -p /gatkCloneMountPoint" >> /root/run_unit_tests.sh 59 60WORKDIR /root 61RUN cp -r /root/run_unit_tests.sh /gatk 62RUN cp -r gatk.jar /gatk 63ENV CLASSPATH /gatk/gatk.jar:$CLASSPATH 64 65# Start GATK Python environment 66 67WORKDIR /gatk 68RUN chmod -R a+rw /gatk 69ENV PATH $CONDA_PATH/envs/gatk/bin:$CONDA_PATH/bin:$PATH 70RUN conda env create -n gatk -f /gatk/gatkcondaenv.yml && \ 71 echo "source activate gatk" >> /gatk/gatkenv.rc && \ 72 echo "source /gatk/gatk-completion.sh" >> /gatk/gatkenv.rc && \ 73 conda clean -afy && \ 74 find /opt/miniconda/ -follow -type f -name '*.a' -delete && \ 75 find /opt/miniconda/ -follow -type f -name '*.pyc' -delete && \ 76 rm -rf /root/.cache/pip 77 78CMD ["bash", "--init-file", "/gatk/gatkenv.rc"] 79 80# End GATK Python environment 81 82ENV PATH /gatk:$PATH 83