From a0cc08f1d49ac33518770893439a77309be70c6d Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 14 Sep 2026 07:35:06 -0700 Subject: [PATCH 1/2] Force version of freemarker dependency coming from picard --- SequenceAnalysis/build.gradle | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 532829490..f906805f6 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -22,6 +22,7 @@ import java.util.regex.Matcher configurations.all { resolutionStrategy { force "org.glassfish.jaxb:jaxb-runtime:${jaxbVersion}" + force "org.freemarker:freemarker:2.3.35" // until picard version is updated use this version or later } } @@ -135,7 +136,7 @@ dependencies { BuildUtils.addExternalDependency( project, new ExternalDependency( - "com.github.broadinstitute:picard:3.4.0", + "com.github.broadinstitute:picard:3.5.0", "Picard Tools Lib", "PicardTools", "https://github.com/broadinstitute/picard", From 715217b0a96900bdc09ebd657037067c6b225cbe Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 14 Sep 2026 09:38:43 -0700 Subject: [PATCH 2/2] Revert update to picard version for troubleshooting --- SequenceAnalysis/build.gradle | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index f906805f6..dc0958380 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -22,7 +22,7 @@ import java.util.regex.Matcher configurations.all { resolutionStrategy { force "org.glassfish.jaxb:jaxb-runtime:${jaxbVersion}" - force "org.freemarker:freemarker:2.3.35" // until picard version is updated use this version or later + force "org.freemarker:freemarker:2.3.35" // until picard version is updated to use this version or later } } @@ -136,7 +136,7 @@ dependencies { BuildUtils.addExternalDependency( project, new ExternalDependency( - "com.github.broadinstitute:picard:3.5.0", + "com.github.broadinstitute:picard:3.4.0", "Picard Tools Lib", "PicardTools", "https://github.com/broadinstitute/picard",