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