git: 4dfff98fb505 - main - biology/picard-tools: Update to 3.5.0

From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Thu, 10 Sep 2026 11:51:52 UTC 
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=4dfff98fb5054dbd241494de002e1fd1c1d9447c

commit 4dfff98fb5054dbd241494de002e1fd1c1d9447c
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-10 11:51:02 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-10 11:51:02 +0000

    biology/picard-tools: Update to 3.5.0
    
    Numerous improvements since 2.22.9
    Changes: biology/picard-tools: Update to 3.5.0
    
    Reported by:    Repology
---
 biology/picard-tools/Makefile        | 7 +++----
 biology/picard-tools/distinfo        | 6 +++---
 biology/picard-tools/files/picard.in | 0
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/biology/picard-tools/Makefile b/biology/picard-tools/Makefile
index 245a0a5c3d00..bf250a7fe878 100644
--- a/biology/picard-tools/Makefile
+++ b/biology/picard-tools/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	picard
-DISTVERSION=	2.22.9
-PORTREVISION=	2
+DISTVERSION=	3.5.0
 CATEGORIES=	biology java
 MASTER_SITES=	http://github.com/broadinstitute/picard/releases/download/${PORTVERSION}/
 PKGNAMESUFFIX=	-tools
@@ -9,13 +8,13 @@ EXTRACT_SUFX=	.jar
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	CLI tools for manipulating high-throughput sequencing (HTS) data
-WWW=		https://broadinstitute.github.io/picard/
+WWW=		https://github.com/broadinstitute/picard
 
 LICENSE=	MIT
 
 RUN_DEPENDS=	samtools:biology/samtools
 
-USES=		java
+USES=		java:run
 
 CONFLICTS_INSTALL=	picard # bin/picard
 
diff --git a/biology/picard-tools/distinfo b/biology/picard-tools/distinfo
index a4e72523df98..0d8391e18d6f 100644
--- a/biology/picard-tools/distinfo
+++ b/biology/picard-tools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1591387929
-SHA256 (picard.jar) = a3d8830f68443a745cca9e1bab9adbc1c435fe3639709b118f5a89858a12a362
-SIZE (picard.jar) = 17520128
+TIMESTAMP = 1788997123
+SHA256 (picard.jar) = b7d97861c3a54ba5a421f5a317f38382f955803862d30ef4aca2bcdc54943631
+SIZE (picard.jar) = 64763062
diff --git a/biology/picard-tools/files/picard.in b/biology/picard-tools/files/picard.in
old mode 100644
new mode 100755