git: 779b0ad35f96 - main - biology/gmap: Update to 2025.07.31

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=779b0ad35f96ea5877c01c459588675319230526

commit 779b0ad35f96ea5877c01c459588675319230526
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-04 14:22:38 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-04 14:22:38 +0000

    biology/gmap: Update to 2025.07.31
    
    Numerous fixes and enhancements since 2020.09.12
    Changes: http://research-pub.gene.com/gmap/
    
    Reported by:    Repology
---
 biology/gmap/Makefile  | 9 ++++++---
 biology/gmap/distinfo  | 6 +++---
 biology/gmap/pkg-plist | 3 ++-
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile
index acde8f9f3f1c..0022e9cf09c4 100644
--- a/biology/gmap/Makefile
+++ b/biology/gmap/Makefile
@@ -1,20 +1,23 @@
 PORTNAME=	gmap
-PORTVERSION=	2020.09.12
+PORTVERSION=	2025.07.31
 CATEGORIES=	biology
 MASTER_SITES=	http://research-pub.gene.com/gmap/src/
 DISTNAME=	${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genomic Mapping and Alignment Program for mRNA and EST Sequences
-WWW=		http://www.gene.com/share/gmap
+WWW=		https://github.com/genentech/gmap-gsnap \
+		http://research-pub.gene.com/gmap/
 
 LICENSE=	GMAP
 LICENSE_NAME=	GMAP License
 LICENSE_FILE=	${WRKSRC}/COPYING
 LICENSE_PERMS=	dist-mirror pkg-mirror auto-accept
 
+# FIXME: Source shows support for other platforms, but build fails on
+# aarch64 trying to use asm(bsr)
 ONLY_FOR_ARCHS=		amd64 i386 powerpc64le
-ONLY_FOR_ARCHS_REASON=	upstream supports only x86 and possibly POWER8
+ONLY_FOR_ARCHS_REASON=	Upstream supports only x86 and possibly POWER8
 
 USES=		gmake perl5
 GNU_CONFIGURE=	yes
diff --git a/biology/gmap/distinfo b/biology/gmap/distinfo
index 9ed16c632335..b02015bce13d 100644
--- a/biology/gmap/distinfo
+++ b/biology/gmap/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1600434673
-SHA256 (gmap-gsnap-2020-09-12.tar.gz) = 9f267d8d165a99b8cb41a22217ed9f8a987ba8b8f8303b0ae867d3e8bf96cef3
-SIZE (gmap-gsnap-2020-09-12.tar.gz) = 4470731
+TIMESTAMP = 1788268502
+SHA256 (gmap-gsnap-2025-07-31.tar.gz) = cc7212446683785a5b94aba79861212360d421ea409cd7cbf287f1dc63ed844d
+SIZE (gmap-gsnap-2025-07-31.tar.gz) = 5231678
diff --git a/biology/gmap/pkg-plist b/biology/gmap/pkg-plist
index 65b5bd55c23b..0ca75dba5798 100644
--- a/biology/gmap/pkg-plist
+++ b/biology/gmap/pkg-plist
@@ -5,6 +5,7 @@ bin/dbsnp_iit
 bin/ensembl_genes
 bin/fa_coords
 bin/get-genome
+bin/gff3_exons
 bin/gff3_genes
 bin/gff3_introns
 bin/gff3_splicesites
@@ -20,6 +21,7 @@ bin/gsnap
 bin/gsnap.nosimd
 bin/gsnapl
 bin/gsnapl.nosimd
+bin/gtf_exons
 bin/gtf_genes
 bin/gtf_introns
 bin/gtf_splicesites
@@ -33,7 +35,6 @@ bin/md_coords
 bin/psl_genes
 bin/psl_introns
 bin/psl_splicesites
-bin/sam_sort
 bin/snpindex
 bin/trindex
 bin/vcf_iit