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Add R to the installed picard modules #282

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Merged
EddieLF merged 1 commit into from
Feb 26, 2026
Merged

Add R to the installed picard modules #282

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5 changes: 3 additions & 2 deletions images/picard/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,15 @@ RUN wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | \
tar -xvj -C /usr/local/bin --strip-components=1 bin/micromamba && \
chmod +x /usr/local/bin/micromamba

# Install samtools, gcloud-sdk, and the Java Runtime (JRE)
# Install samtools, gcloud-sdk, R, and the Java Runtime (JRE)
# We use 'openjdk' here because the JAR needs a Java environment to run.
RUN mkdir -p ${MAMBA_ROOT_PREFIX} && \
micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} \
-c bioconda -c conda-forge \
samtools \
google-cloud-sdk \
openjdk=17 && \
openjdk=17 \
r-base && \
micromamba clean --all --yes

# Copy the JAR from the builder stage and set up the entrypoint script
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