Reduced gatk base image layers from 20 to just 3.

scripts/docker/gatkbase/Dockerfile

@@ -3,10 +3,14 @@
 # NOTE: If you update the ubuntu version make sure to update the samtools/bcftools/bedtools versions in the README
 FROM ubuntu:22.04
 
+# Set environment variables.
 # Avoid interactive prompts during apt installs/upgrades
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND="noninteractive" HOME="/root" JAVA_LIBRARY_PATH="/usr/lib/jni" DOWNLOAD_DIR="/downloads" CONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh" CONDA_SHA256="c7a34df472feb69805b64df6e8db58363c5ccab41cd3b40b07e3e6dfb924359a" CONDA_PATH="/opt/miniconda" PATH="/opt/miniconda/bin:$PATH"
+
+# Define working directory.
+WORKDIR /root
 
-#### Basic image utilities
+#### Basic image utilities, google cloud support, and miniconda
 RUN apt update && \
     apt full-upgrade -y && \
     apt install -y --no-install-recommends \
@@ -32,12 +36,9 @@ RUN apt update && \
     apt -y clean  && \
     apt -y autoclean  && \
     apt -y autoremove && \
-    rm -rf /var/lib/apt/lists/*
-
-RUN java -version
-
-#### Specific for google cloud support
-RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" \
+    rm -rf /var/lib/apt/lists/* && \
+    java -version && \
+    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" \
     | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg \
     | apt-key --keyring /usr/share/keyrings/cloud.google.gpg  add - && \
     apt update -y && \
@@ -49,26 +50,8 @@ RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.c
 #  Remove the anthos cli tool and related files since they are very large and we / anyone using the docker are unlikely to use them
 #  Remove the bundled python because we have python installed separately
     rm -rf /usr/lib/google-cloud-sdk/bin/anthoscli /usr/lib/google-cloud-sdk/platform/anthoscli_licenses /usr/lib/google-cloud-sdk/platform/bundledpythonunix && \
-    find / -wholename "*__pycache__/*.pyc" -exec rm {} + 
-
-# Set environment variables.
-ENV HOME /root
-
-# Define working directory.
-WORKDIR /root
-
-# Define default command.
-CMD ["bash"]
-
-ENV JAVA_LIBRARY_PATH /usr/lib/jni
-
-# Install miniconda
-ENV DOWNLOAD_DIR /downloads
-ENV CONDA_URL https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh
-ENV CONDA_SHA256 "c7a34df472feb69805b64df6e8db58363c5ccab41cd3b40b07e3e6dfb924359a"
-ENV CONDA_PATH /opt/miniconda
-ENV PATH $CONDA_PATH/bin:$PATH
-RUN mkdir $DOWNLOAD_DIR && \
+    find / -wholename "*__pycache__/*.pyc" -exec rm {} + && \
+    mkdir $DOWNLOAD_DIR && \
     wget -nv -O $DOWNLOAD_DIR/miniconda.sh $CONDA_URL && \
     test "$(sha256sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS=' ' -v ORS='' '{print $1}')" = "$CONDA_SHA256" && \
     bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \
@@ -77,3 +60,26 @@ RUN mkdir $DOWNLOAD_DIR && \
     conda config --set auto_update_conda false && \
     conda config --set solver libmamba && \
     rm -rf /root/.cache/pip
+
+# Set environment variables.
+# ENV HOME /root
+
+# ENV JAVA_LIBRARY_PATH /usr/lib/jni
+
+# Install miniconda
+# ENV DOWNLOAD_DIR /downloads
+# ENV CONDA_URL https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh
+# ENV CONDA_SHA256 "c7a34df472feb69805b64df6e8db58363c5ccab41cd3b40b07e3e6dfb924359a"
+# ENV CONDA_PATH /opt/miniconda
+# ENV PATH $CONDA_PATH/bin:$PATH
+# RUN mkdir $DOWNLOAD_DIR && \
+#     wget -nv -O $DOWNLOAD_DIR/miniconda.sh $CONDA_URL && \
+#     test "$(sha256sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS=' ' -v ORS='' '{print $1}')" = "$CONDA_SHA256" && \
+#     bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \
+#     rm $DOWNLOAD_DIR/miniconda.sh && \
+#     conda clean -afy && \
+#     conda config --set auto_update_conda false && \
+#     conda config --set solver libmamba && \
+#     rm -rf /root/.cache/pip
+# Define default command.
+CMD ["bash"]