Add new GATK image built from nightly snapshot 2026-03-01

images/gatk_nightly/Dockerfile

@@ -0,0 +1,80 @@
+# Build from the Nightly Snapshot of GATK from 2026-03-01
+ARG VERSION=4.6.2.0-21-ge8c49f600-NIGHTLY-SNAPSHOT
+
+# Stage 1: Base image with common dependencies
+FROM australia-southeast1-docker.pkg.dev/cpg-common/images/gatk:${VERSION} AS base
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y \
+        apt-transport-https \
+        bzip2 \
+        ca-certificates \
+        curl \
+        git \
+        gnupg \
+        jq \
+        libgomp1 \
+        procps \
+        rsync \
+        software-properties-common \
+        unzip \
+        wget \
+        zip && \
+    rm -rf /var/lib/apt/lists/*
+
+# Stage 2: Compiler stage (Build BCFtools)
+FROM base AS compiler
+
+ARG BCFTOOLS_VERSION=1.22
+RUN apt-get update && apt-get install -y \
+        gcc \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        liblzma-dev \
+        libssl-dev \
+        make \
+        pkg-config \
+        zlib1g-dev && \
+    wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+    tar -xf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+    cd bcftools-${BCFTOOLS_VERSION} && \
+    # Neutralize Conda paths for clean compilation
+    export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+    unset CPATH C_INCLUDE_PATH CPLUS_INCLUDE_PATH LIBRARY_PATH && \
+    PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig ./configure --enable-libcurl --enable-s3 --enable-gcs && \
+    make && \
+    strip bcftools plugins/*.so && \
+    make -C htslib-${BCFTOOLS_VERSION} DESTDIR=/bcftools_install install
+
+# Stage 3: Final Runtime Image
+FROM base
+
+# Metadata for better maintainability
+LABEL description="GATK with BCFtools and Google Cloud CLI"
+
+# Copy everything installed under /usr/local in one go
+COPY --from=compiler /bcftools_install/usr/local/ /usr/local/
+
+# Install Google Cloud CLI and runtime libraries for BCFtools
+RUN apt-get update && \
+    # 1. Ensure the keyrings directory exists
+    mkdir -p /usr/share/keyrings && \
+    # 2. Add Google Cloud repo
+    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" \
+    > /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    # 3. Use curl + gpg with --yes (to overwrite) and --batch
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | \
+    gpg --batch --yes --dearmor -o /usr/share/keyrings/cloud.google.gpg && \
+    # 4. Final update and install
+    apt-get update && \
+    apt-get install -y --no-install-recommends \
+        google-cloud-cli \
+        libcurl4 \
+        libgomp1 \
+        zlib1g \
+        libbz2-1.0 \
+        liblzma5 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*