diff --git a/build.gradle b/build.gradle
index 203e3982faa..67d4fab40b3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -11,7 +11,7 @@ plugins {
     id "application"    // provides installDist
     id 'maven-publish'
     id 'signing'
-    id "jacoco"
+//    id "jacoco"
     id "de.undercouch.download" version "5.4.0" //used for downloading GSA lib
     id "com.github.johnrengelman.shadow" version "8.1.1"    //used to build the shadow and sparkJars
     id "com.github.ben-manes.versions" version "0.12.0" //used for identifying dependencies that need updating
@@ -625,18 +625,19 @@ task bundle(type: Zip) {
     }
 }
 
-jacocoTestReport {
-    dependsOn test
-
-    group = "Reporting"
-    description = "Generate Jacoco coverage reports after running tests."
-    getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
-
-    reports {
-        xml.required = true
-        html.required = true
-    }
-}
+//jacocoTestReport {
+//    dependsOn test
+//
+//    group = "Reporting"
+//    description = "Generate Jacoco coverage reports after running tests."
+//    getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
+//
+//    reports {
+//        xml.required = true
+//        html.required = true
+//    }
+//}
+//}
 
 task condaStandardEnvironmentDefinition(type: Copy) {
     from "scripts"
diff --git a/scripts/docker/dockertest.gradle b/scripts/docker/dockertest.gradle
index 692bc945db9..35da49320cb 100644
--- a/scripts/docker/dockertest.gradle
+++ b/scripts/docker/dockertest.gradle
@@ -8,7 +8,7 @@ buildscript {
 
 plugins {
     id "java"           // set up default java compile and test tasks
-    id "jacoco"
+//    id "jacoco"
 }
 
 repositories {
@@ -113,9 +113,9 @@ def getJVMArgs(runtimeAddOpens, testAddOpens) {
 
 test {
     jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
-    jacoco {
-        jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
-    }
+//    jacoco {
+//        jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
+//    }
 }
 
 task testOnPackagedReleaseJar(type: Test){
@@ -153,22 +153,22 @@ task testOnPackagedReleaseJar(type: Test){
 
 // Task intended to collect coverage data from testOnPackagedReleaseJar executed inside the docker image
 // the classpath for these tests is set at execution time for testOnPackagedReleaseJar
-task jacocoTestReportOnPackagedReleaseJar(type: JacocoReport) {
-    String sourceFiles = "$System.env.SOURCE_DIR"
-    String testClassesUnpacked = "$System.env.CP_DIR"
-
-    dependsOn testOnPackagedReleaseJar
-    executionData testOnPackagedReleaseJar
-    additionalSourceDirs.setFrom(sourceSets.main.allJava.srcDirs)
-
-    sourceDirectories.setFrom(sourceFiles)
-    classDirectories.setFrom(testClassesUnpacked)
-
-    group = "Reporting"
-    description = "Generate Jacoco coverage reports after running tests inside the docker image."
-
-    reports {
-        xml.required = true
-        html.required = true
-    }
-}
+//task jacocoTestReportOnPackagedReleaseJar(type: JacocoReport) {
+//    String sourceFiles = "$System.env.SOURCE_DIR"
+//    String testClassesUnpacked = "$System.env.CP_DIR"
+//
+//    dependsOn testOnPackagedReleaseJar
+//    executionData testOnPackagedReleaseJar
+//    additionalSourceDirs.setFrom(sourceSets.main.allJava.srcDirs)
+//
+//    sourceDirectories.setFrom(sourceFiles)
+//    classDirectories.setFrom(testClassesUnpacked)
+//
+//    group = "Reporting"
+//    description = "Generate Jacoco coverage reports after running tests inside the docker image."
+//
+//    reports {
+//        xml.required = true
+//        html.required = true
+//    }
+//}
diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template
index 4fa5ae1d805..b3b4c72ad01 100644
--- a/scripts/gatkcondaenv.yml.template
+++ b/scripts/gatkcondaenv.yml.template
@@ -30,6 +30,7 @@ dependencies:
 - conda-forge::scipy=1.11.4
 - conda-forge::h5py=3.10.0
 - conda-forge::pytorch=2.1.0=*mkl*100
+- conda-forge::pytorch-lightning=2.4.0   # supports Pytorch >= 2.1 and <= 2.4
 - conda-forge::scikit-learn=1.3.2
 - conda-forge::matplotlib=3.8.2
 - conda-forge::pandas=2.1.3