From 937ff90ce71c6639fb0aa2977b4f539d5db13ef5 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 27 Sep 2024 16:12:23 -0400
Subject: [PATCH] Add pytorch-lightning to GATK conda env, temporarily disable
 jacoco in build.gradle

---
 build.gradle                      | 27 ++++++++++++++-------------
 scripts/gatkcondaenv.yml.template |  1 +
 2 files changed, 15 insertions(+), 13 deletions(-)

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/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