<commit_before># Using OpenJDK 8
FROM broadinstitute/gatk:gatkbase-1.2.3
ARG DRELEASE

ADD . /gatk

WORKDIR /gatk
RUN /gatk/gradlew clean compileTestJava installAll 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<commit_msg>Fixed the docker to run using the Jar rather than the build script (#4476)<commit_after># 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
{'fraction_non_alphanumeric': 0.0864903502501787, 'fraction_numerical': 0.008577555396711936, 'mean_word_length': 3.895104895104895, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2513603', 'n_tokens_mistral': 528, 'n_tokens_neox': 498, 'n_words': 172}