Update base image to 3.0.0(#8228)

* Updating the base image to include Java 17
* Updating ubuntu to the newest 18.04 release

.dockerignore

@@ -1,3 +1,4 @@
 # These are files that for whatever reason we don't want to include in our distribution docker images
 src/test/resources
 src/test/resources/*
+build/

Dockerfile

@@ -1,5 +1,5 @@
 # stage 1 for constructing the GATK zip
-FROM broadinstitute/gatk:gatkbase-2.3.0 AS gradleBuild
+FROM broadinstitute/gatk:gatkbase-3.0.0 AS gradleBuild
 LABEL stage=gatkIntermediateBuildImage
 ARG RELEASE=false
 
@@ -16,46 +16,19 @@ RUN add-apt-repository universe && apt update
 RUN apt-get --assume-yes install git-lfs
 RUN git lfs install --force
 
-##Get Java 17 temurin JDK
-#RUN apt update && apt upgrade
-RUN apt install wget
-RUN wget https://github.com/adoptium/temurin17-binaries/releases/download/jdk-17.0.6%2B10/OpenJDK17U-jdk_x64_linux_hotspot_17.0.6_10.tar.gz
-RUN tar -xvf OpenJDK17U-jdk_x64_linux_hotspot_17.*.tar.gz
-RUN mv jdk-17.0.6+10 /opt/
-#
-ENV JAVA_HOME /opt/jdk-17.0.6+10
-ENV PATH $JAVA_HOME/bin:$PATH
-RUN echo $JAVA_HOME
-RUN update-alternatives --install /usr/bin/java java /opt/jdk-17.0.6+10/bin/java 1
-RUN java -version
-
 #Download only resources required for the build, not for testing
 RUN git lfs pull --include src/main/resources/large
 
 RUN export GRADLE_OPTS="-Xmx4048m -Dorg.gradle.daemon=false" && /gatk/gradlew clean collectBundleIntoDir shadowTestClassJar shadowTestJar -Drelease=$RELEASE
 RUN cp -r $( find /gatk/build -name "*bundle-files-collected" )/ /gatk/unzippedJar/
 RUN unzip -o -j $( find /gatk/unzippedJar -name "gatkPython*.zip" ) -d /gatk/unzippedJar/scripts
 
-# Using OpenJDK 8
-FROM broadinstitute/gatk:gatkbase-2.3.0
+FROM broadinstitute/gatk:gatkbase-3.0.0
 
 RUN rm /etc/apt/sources.list.d/google-cloud-sdk.list
 RUN apt update
 RUN apt-key list
 
-#Get Java 17 temurin JDK
-#RUN apt update && apt upgrade
-RUN apt install wget
-RUN wget https://github.com/adoptium/temurin17-binaries/releases/download/jdk-17.0.6%2B10/OpenJDK17U-jdk_x64_linux_hotspot_17.0.6_10.tar.gz
-RUN tar -xvf OpenJDK17U-jdk_x64_linux_hotspot_17.*.tar.gz
-RUN mv jdk-17.0.6+10 /opt/
-
-ENV JAVA_HOME /opt/jdk-17.0.6+10
-ENV PATH $JAVA_HOME/bin:$PATH
-RUN echo $JAVA_HOME
-RUN update-alternatives --install /usr/bin/java java /opt/jdk-17.0.6+10/bin/java 1
-RUN java -version
-
 WORKDIR /gatk
 
 # Location of the unzipped gatk bundle files

scripts/docker/gatkbase/Dockerfile

@@ -1,12 +1,12 @@
-# Using OpenJDK 8
+# Using OpenJDK 17
 # This Dockerfile does not require any files that are in the GATK4 repo.
 FROM ubuntu:18.04
 
 #### Basic image utilities
 RUN apt-get update && \
     apt-get upgrade -y && \
     apt-get install -y --no-install-recommends \
-    python \
+    python3 \
     wget \
     curl \
     bc \
@@ -15,23 +15,27 @@ RUN apt-get update && \
     less \
     bedtools \
     samtools \
-    openjdk-8-jdk \
     tabix \
     gpg-agent \
     build-essential \
+    openjdk-17-jdk \
     software-properties-common && \
     apt-get -y clean  && \
     apt-get -y autoclean  && \
     apt-get -y autoremove
 
+RUN java -version
+
 #### Specific for google cloud support
-RUN export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
-    echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO 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 add - && \
-    apt-get update -y && apt-get install google-cloud-sdk -y && \
+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-get -y clean
-###########
+    find / -wholename "*__pycache__/*.pyc" -exec rm {} + 
 
 # Set environment variables.
 ENV HOME /root
@@ -43,9 +47,6 @@ WORKDIR /root
 CMD ["bash"]
 
 ENV JAVA_LIBRARY_PATH /usr/lib/jni
-ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/
-
-RUN java -version
 
 # Install miniconda
 ENV DOWNLOAD_DIR /downloads
@@ -56,7 +57,12 @@ 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" && \
     bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \
-    rm $DOWNLOAD_DIR/miniconda.sh
+    rm $DOWNLOAD_DIR/miniconda.sh && \
+    ${CONDA_PATH}/bin/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
+
 
 # Deleting unneeded caches
 RUN rm -rf /var/lib/apt/lists/*