git: 803f55e390e8 - main - biology/gatk: update 4.6.1.0 → 4.6.2.0

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=803f55e390e82974387403ff9a21e5556625424c

commit 803f55e390e82974387403ff9a21e5556625424c
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-08-27 17:24:34 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-08-27 17:24:54 +0000

    biology/gatk: update 4.6.1.0 → 4.6.2.0
---
 biology/gatk/Makefile         | 10 +++++-----
 biology/gatk/distinfo         | 10 +++++-----
 biology/gatk/files/gatk.sh.in |  4 ++--
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile
index 41df894298f4..49a990d3f216 100644
--- a/biology/gatk/Makefile
+++ b/biology/gatk/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	gatk
-DISTVERSION=	4.6.1.0
-PORTREVISION=	1
+DISTVERSION=	4.6.2.0
 CATEGORIES=	biology java
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
@@ -31,7 +30,7 @@ NO_ARCH=	yes
 DEPS_CACHE_DIR=	${WRKDIR}
 
 TEST_ENV=	${MAKE_ENV} \
-		JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \
+		JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \
 		GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
 PLIST_FILES=	bin/${PORTNAME} \
@@ -117,9 +116,10 @@ do-install:
 
 do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space
 	@cd ${WRKSRC} && \
-		${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test
+		${SETENV} ${TEST_ENV} gradle8 test
 
-# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940
+# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940
+# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped
 # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib
 
 .include <bsd.port.mk>
diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo
index 2494dc43dd72..42fbad5e8a91 100644
--- a/biology/gatk/distinfo
+++ b/biology/gatk/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1730356703
-SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad
-SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997
-SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378
-SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196
+TIMESTAMP = 1756227460
+SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77
+SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113
+SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866
+SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606
diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in
index d3d5c0f7bf5a..20c6c16d5164 100644
--- a/biology/gatk/files/gatk.sh.in
+++ b/biology/gatk/files/gatk.sh.in
@@ -23,5 +23,5 @@ fi
 
 # execute the command
 # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient)
-JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \
-%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"
+JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \
+%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"