1E-16 epsilon, conda 23.10.0

Dockerfile

@@ -1,4 +1,4 @@
-ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6
+ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6-sl
 
 # stage 1 for constructing the GATK zip
 FROM ${BASE_DOCKER} AS gradleBuild

scripts/docker/gatkbase/Dockerfile

@@ -62,8 +62,8 @@ 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_SHA256 "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 && \
@@ -72,4 +72,6 @@ RUN mkdir $DOWNLOAD_DIR && \
     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

scripts/docker/gatkbase/build_docker_base.sh

@@ -4,10 +4,11 @@
 set -e
 
 
+
 REPO=broadinstitute
 PROJECT=gatk
 VERSION=2.3.0
-FULL_PATH=${REPO}/${PROJECT}:gatkbase-${VERSION}
+FULL_PATH=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6-sl
 
 #################################################
 # Parsing arguments

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java

@@ -43,7 +43,7 @@ public static void runH5Diff(final String expected, final String actual) {
         // -r: Report mode. Print the differences.
         // --use-system-epsilon: Return a difference if and only if the difference between two data values exceeds
         //                       the system value for epsilon.
-        final String[] command = new String[] { "h5diff", "-r", "--use-system-epsilon", expected, actual };
+        final String[] command = new String[] { "h5diff", "-r", "-p", "1E-16", expected, actual };
 
         runProcessAndCaptureOutputInExceptionMessage(controller, command);
     }

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java

@@ -45,7 +45,7 @@ public static void runH5Diff(final String expected, final String actual) {
         // -r: Report mode. Print the differences.
         // --use-system-epsilon: Return a difference if and only if the difference between two data values exceeds
         //                       the system value for epsilon.
-        final String[] command = new String[] { "h5diff", "-r", "--use-system-epsilon", expected, actual };
+        final String[] command = new String[] { "h5diff", "-r", "-p", "1E-16", expected, actual };
 
         runProcessAndCaptureOutputInExceptionMessage(controller, command);
     }