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Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support #285

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Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support #285

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318e0d1
Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support
EddieLF Mar 2, 2026
f7ea0a8
remove R-base install from apt-get install list
EddieLF Mar 2, 2026
0594ca9
Install git-lfs with apt-get install
EddieLF Mar 2, 2026
82009eb
Split out git lfs commands
EddieLF Mar 2, 2026
9d15330
Hardcode version in git clone?
EddieLF Mar 2, 2026
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24 changes: 19 additions & 5 deletions images/gatk/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ RUN apt-get update && \
ca-certificates \
curl \
git \
git-lfs \
gnupg \
jq \
libgomp1 \
Expand Down Expand Up @@ -48,6 +49,7 @@ RUN apt-get update && apt-get install -y \
make -C htslib-$BCFTOOLS_VERSION DESTDIR=/bcftools_install install


# build GATK image from source, using the compiled bcftools binaries and plugins
FROM base

COPY --from=compiler /bcftools_install/usr/local/bin/* /usr/local/bin/
Expand All @@ -62,11 +64,23 @@ RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.
rm -r /var/lib/apt/lists/* && \
rm -r /var/cache/apt/*

# download and install GATK pre-built release
RUN wget -q https://github.com/broadinstitute/gatk/releases/download/4.6.2.0/gatk-4.6.2.0.zip && \
unzip gatk-4.6.2.0.zip && \
rm gatk-4.6.2.0.zip && \
chmod +x /gatk-4.6.2.0/gatk
# Clone GATK source code (including large files with git-lfs) and build the GATK jar file
RUN git clone --branch 4.6.2.0 --depth 1 https://github.com/broadinstitute/gatk.git

RUN git lfs install && \
git lfs pull
# Build GATK with htsjdk 4.3.0 for CRAM v3.1 support
RUN ./gradlew clean printVersion shadowJar -Dhtsjdk.version=4.3.0

ENV PATH=$PATH:/gatk-4.6.2.0
WORKDIR /gatk-4.6.2.0

# Install Miniconda3-py310_23.10.0-1
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh -O /tmp/miniconda.sh && \
bash /tmp/miniconda.sh -p /opt/miniconda -b && \
rm /tmp/miniconda.sh && \
/opt/miniconda/bin/conda clean -afy && \
conda config --set auto_update_conda false && \
conda config --set solver libmamba && \
./gradlew localDevCondaEnv && \
source activate gatk
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