Incorporate base image changes from Sam Lee's PR, fix md5 check, othe…

…r changes

Dockerfile

@@ -1,4 +1,4 @@
-ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc3
+ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc4
 
 # stage 1 for constructing the GATK zip
 FROM ${BASE_DOCKER} AS gradleBuild
@@ -93,8 +93,6 @@ RUN conda env create -n gatk -f /gatk/gatkcondaenv.yml && \
     echo "source activate gatk" >> /gatk/gatkenv.rc && \
     echo "source /gatk/gatk-completion.sh" >> /gatk/gatkenv.rc && \
     conda clean -afy && \
-    find $CONDA_PATH -follow -type f -name '*.a' -delete && \
-    find $CONDA_PATH -follow -type f -name '*.pyc' -delete && \
     rm -rf /root/.cache/pip
 
 CMD ["bash", "--init-file", "/gatk/gatkenv.rc"]

scripts/docker/gatkbase/Dockerfile

@@ -3,11 +3,10 @@
 FROM ubuntu:22.04
 
 #### Basic image utilities
-RUN apt-get update && \
-    apt-get upgrade -y && \
-    apt-get install -y --no-install-recommends \
+RUN apt update && \
+    apt full-upgrade -y && \
+    apt install -y --no-install-recommends \
     python3 \
-    python3-pip \
     wget \
     curl \
     bc \
@@ -21,12 +20,13 @@ RUN apt-get update && \
     git \
     gpg-agent \
     build-essential \
+    libblas-dev \
     openjdk-17-jdk \
     vim \
     software-properties-common && \
-    apt-get -y clean  && \
-    apt-get -y autoclean  && \
-    apt-get -y autoremove && \
+    apt -y clean  && \
+    apt -y autoclean  && \
+    apt -y autoremove && \
     rm -rf /var/lib/apt/lists/*
 
 RUN java -version
@@ -35,11 +35,11 @@ RUN java -version
 RUN 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-get update -y && \
-    apt-get install -y --no-install-recommends google-cloud-cli && \
-    apt-get -y clean  && \
-    apt-get -y autoclean  && \
-    apt-get -y autoremove && \
+    apt update -y && \
+    apt install -y --no-install-recommends google-cloud-cli && \
+    apt -y clean  && \
+    apt -y autoclean  && \
+    apt -y autoremove && \
     rm -rf /var/lib/apt/lists/* && \
 #  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
@@ -59,35 +59,16 @@ ENV JAVA_LIBRARY_PATH /usr/lib/jni
 
 # Install miniconda
 ENV DOWNLOAD_DIR /downloads
-ENV CONDA_URL https://repo.anaconda.com/miniconda/Miniconda3-py310_23.1.0-1-Linux-x86_64.sh
-ENV CONDA_MD5 = "32d73e1bc33fda089d7cd9ef4c1be542616bd8e437d1f77afeeaf7afdb019787"
+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 "`md5sum $DOWNLOAD_DIR/miniconda.sh | awk -v FS='  ' '{print $1}'` = $CONDA_MD5" && \
+    test "$(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 config --set auto_update_conda false && \
+    conda config --set solver libmamba && \
     conda clean -afy && \
-    find /opt/miniconda/ -follow -type f -name '*.a' -delete && \
-    find /opt/miniconda/ -follow -type f -name '*.pyc' -delete && \
     rm -rf /root/.cache/pip
-
-# Install miniconda
-# Following the instructions from https://docs.conda.io/projects/conda/en/latest/user-guide/install/rpm-debian.html
-# Note that this *does* install just miniconda, despite the package being named "conda"
-# RUN curl https://repo.anaconda.com/pkgs/misc/gpgkeys/anaconda.asc | gpg --dearmor > /tmp/conda.gpg && \
-#    install -o root -g root -m 644 /tmp/conda.gpg /usr/share/keyrings/conda-archive-keyring.gpg && \
-#    gpg --keyring /usr/share/keyrings/conda-archive-keyring.gpg --no-default-keyring --fingerprint 34161F5BF5EB1D4BFBBB8F0A8AEB4F8B29D82806 && \
-#    rm /tmp/conda.gpg && \
-#    echo "deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main" > /etc/apt/sources.list.d/conda.list && \
-#    apt update && \
-#    apt install conda && \
-#    apt -y clean  && \
-#    apt -y autoclean  && \
-#    apt -y autoremove && \
-#    . /opt/conda/etc/profile.d/conda.sh && \
-#    conda -V
-#
-# ENV CONDA_PATH /opt/conda
-# ENV PATH $CONDA_PATH/bin:$PATH