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Date: Sun, 4 Jun 2023 22:03:56 GMT
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To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org,
dev-commits-ports-main@FreeBSD.org
From: Yuri Victorovich <yuri@FreeBSD.org>
Subject: git: 6541d6f389c9 - main - =?utf-8?Q?biology/gatk:=20Update=204.3.0.0=20=E2=86=92=204.4.0.0?=
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The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=6541d6f389c9d95818959222dadbab3d25d8eb08
commit 6541d6f389c9d95818959222dadbab3d25d8eb08
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-06-04 22:02:58 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-06-04 22:02:58 +0000
biology/gatk: Update 4.3.0.0 → 4.4.0.0
---
biology/gatk/Makefile | 8 +++++---
biology/gatk/distinfo | 10 +++++-----
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile
index ee69b70e3cec..daf9eb32ae98 100644
--- a/biology/gatk/Makefile
+++ b/biology/gatk/Makefile
@@ -1,5 +1,5 @@
PORTNAME= gatk
-DISTVERSION= 4.3.0.0
+DISTVERSION= 4.4.0.0
CATEGORIES= biology java
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
@@ -12,7 +12,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
BROKEN_FreeBSD_12_powerpc64= fails to build: String index out of range: -1
-BUILD_DEPENDS= gradle:devel/gradle
+BUILD_DEPENDS= gradle761:devel/gradle761
USES= gettext-runtime
USE_JAVA= yes
@@ -32,6 +32,8 @@ DEPS_CACHE_DIR= ${WRKDIR}
PLIST_FILES= bin/${PORTNAME} \
${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
+BINARY_ALIAS= java=${JAVA}
+
# TODO additionally fetch git-lfs files: https://github.com/broadinstitute/gatk/issues/6395
# to rebuild the deps archive:
@@ -86,7 +88,7 @@ post-extract: # need a separate extract step because the cache is in /tmp, and n
.endif
do-build:
- @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
+ cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle761 \
--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
${GRADLE_ARGS} --build-cache localJar
diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo
index 816c61bd9752..2c162723ff0d 100644
--- a/biology/gatk/distinfo
+++ b/biology/gatk/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1669519665
-SHA256 (gatk-4.3.0.0-deps.tar.gz) = 2cecff5daf25ab55da7cea574801f1f802ac60337438f209067563c5deb13bd8
-SIZE (gatk-4.3.0.0-deps.tar.gz) = 552787501
-SHA256 (broadinstitute-gatk-4.3.0.0_GH0.tar.gz) = 93f8ab1e0380d023e1e7eed9d5a0cce0e606679ad91c58e8ffee08222ce92443
-SIZE (broadinstitute-gatk-4.3.0.0_GH0.tar.gz) = 98743503
+TIMESTAMP = 1685914727
+SHA256 (gatk-4.4.0.0-deps.tar.gz) = 1122d2c0d79048b3a2c507262a76af98b1f1c6e9e70c6d459f458fa33939a58c
+SIZE (gatk-4.4.0.0-deps.tar.gz) = 717202736
+SHA256 (broadinstitute-gatk-4.4.0.0_GH0.tar.gz) = 026498bdb1e07041abc74e26c84e681d77212a3d3dd66c83249957a0518e4bfe
+SIZE (broadinstitute-gatk-4.4.0.0_GH0.tar.gz) = 100594033