| ARG RELEASE |
| ARG LAUNCHPAD_BUILD_ARCH |
| LABEL org.opencontainers.image.ref.name=ubuntu |
| LABEL org.opencontainers.image.version=22.04 |
| ADD file:36d444e2cede3abe58191dcf28890b874c0908f5259bf7e8855338555701c4c5 in / |
| CMD ["/bin/bash"] |
| ENV DEBIAN_FRONTEND=noninteractive |
| /bin/sh -c apt update && apt full-upgrade -y && apt install -y --no-install-recommends python3 python3-pip wget curl bc unzip bzip2 less bedtools samtools bcftools tabix jq git gpg-agent build-essential openjdk-17-jdk vim software-properties-common && apt -y clean && apt -y autoclean && apt -y autoremove && rm -rf /var/lib/apt/lists/* |
| /bin/sh -c java -version |
| /bin/sh -c echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && apt update -y && apt install -y --no-install-recommends google-cloud-cli && apt -y clean && apt -y autoclean && apt -y autoremove && rm -rf /var/lib/apt/lists/* && rm -rf /usr/lib/google-cloud-sdk/bin/anthoscli /usr/lib/google-cloud-sdk/platform/anthoscli_licenses /usr/lib/google-cloud-sdk/platform/bundledpythonunix && find / -wholename "*__pycache__/*.pyc" -exec rm {} + |
| ENV HOME=/root |
| WORKDIR /root |
| CMD ["bash"] |
| ENV JAVA_LIBRARY_PATH=/usr/lib/jni |
| ENV DOWNLOAD_DIR=/downloads |
| ENV CONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh |
| ENV CONDA_SHA256=c7a34df472feb69805b64df6e8db58363c5ccab41cd3b40b07e3e6dfb924359a |
| ENV CONDA_PATH=/opt/miniconda |
| ENV PATH=/opt/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin |
| /bin/sh -c mkdir $DOWNLOAD_DIR && wget -nv -O $DOWNLOAD_DIR/miniconda.sh $CONDA_URL && test "$(sha256sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS=' ' -v ORS='' '{print $1}')" = "$CONDA_SHA256" && bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && rm $DOWNLOAD_DIR/miniconda.sh && conda clean -afy && conda config --set auto_update_conda false && conda config --set solver libmamba && rm -rf /root/.cache/pip |
| /bin/sh -c rm /etc/apt/sources.list.d/google-cloud-sdk.list && apt update && apt-key list && apt-get -y clean && apt-get -y autoclean && apt-get -y autoremove && rm -rf /var/lib/apt/lists/* |
| WORKDIR /gatk |
| /bin/sh -c chmod -R a+rw /gatk |
| COPY dir:09a895dc0a04195a24fd3ee2985b37acc9fc9e639e456ab58578a375cf71fd2f in . |
| /bin/sh -c ln -s $( find /gatk -name "gatk*local.jar" ) gatk.jar |
| /bin/sh -c ln -s $( find /gatk -name "gatk*local.jar" ) /root/gatk.jar |
| /bin/sh -c ln -s $( find /gatk -name "gatk*spark.jar" ) gatk-spark.jar |
| WORKDIR /root |
| /bin/sh -c java -jar gatk.jar -h |
| /bin/sh -c mkdir /gatkCloneMountPoint |
| /bin/sh -c mkdir /jars |
| /bin/sh -c mkdir .gradle |
| WORKDIR /gatk |
| ENV CI=true |
| /bin/sh -c echo "source activate gatk" > /root/run_unit_tests.sh && echo "export GATK_DOCKER_CONTAINER=true" >> /root/run_unit_tests.sh && echo "export TEST_JAR=\$( find /jars -name \"gatk*test.jar\" )" >> /root/run_unit_tests.sh && echo "export TEST_DEPENDENCY_JAR=\$( find /jars -name \"gatk*testDependencies.jar\" )" >> /root/run_unit_tests.sh && echo "export GATK_JAR=$( find /gatk -name "gatk*local.jar" )" >> /root/run_unit_tests.sh && echo "export GATK_LAUNCH_SCRIPT=/gatk/gatk" >> /root/run_unit_tests.sh && echo "mkdir /gatk/srcdir" >> /root/run_unit_tests.sh && echo "cp -rp /gatkCloneMountPoint/src/main/java/* /gatk/srcdir" >> /root/run_unit_tests.sh && echo "export SOURCE_DIR=/gatk/srcdir" >> /root/run_unit_tests.sh && echo "export GRADLE_OPTS=\"-Xmx1024m -Dorg.gradle.daemon=false --add-opens java.prefs/java.util.prefs=ALL-UNNAMED\"" >> /root/run_unit_tests.sh && echo "export CP_DIR=/gatk/testClasses" >> /root/run_unit_tests.sh && echo "ln -s /gatkCloneMountPoint/src/ /gatkCloneMountPoint/scripts/docker/src" >> /root/run_unit_tests.sh && echo "ln -s /gatkCloneMountPoint/build/ /gatkCloneMountPoint/scripts/docker/build" >> /root/run_unit_tests.sh && echo "cd /gatk/ && /gatkCloneMountPoint/gradlew -Dfile.encoding=UTF-8 -b /gatkCloneMountPoint/dockertest.gradle testOnPackagedReleaseJar jacocoTestReportOnPackagedReleaseJar -a -p /gatkCloneMountPoint" >> /root/run_unit_tests.sh |
| WORKDIR /root |
| /bin/sh -c cp -r /root/run_unit_tests.sh /gatk |
| /bin/sh -c cp -r gatk.jar /gatk |
| ENV CLASSPATH=/gatk/gatk.jar: |
| WORKDIR /gatk |
| ENV PATH=/opt/miniconda/envs/gatk/bin:/opt/miniconda/bin:/opt/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin |
| /bin/sh -c conda env create -n gatk -f /gatk/gatkcondaenv.yml && echo "source activate gatk" >> /gatk/gatkenv.rc && echo "source /gatk/gatk-completion.sh" >> /gatk/gatkenv.rc && conda clean -afy && rm -rf /root/.cache/pip |
| CMD ["bash" "--init-file" "/gatk/gatkenv.rc"] |
| ENV PATH=/gatk:/opt/miniconda/envs/gatk/bin:/opt/miniconda/bin:/opt/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin |
