git: e3e3bee19927 - main - biology/stacks: Update to 2.68

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e3e3bee19927174745e10cb4188bec6c9b527fae

commit e3e3bee19927174745e10cb4188bec6c9b527fae
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-01-17 22:38:18 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-01-17 22:38:18 +0000

    biology/stacks: Update to 2.68
    
    Numerous fixes and improvements since 2.4
    Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php
    
    PR:             283257
    Reported by:    alster@vinterdalen.se
---
 biology/stacks/Makefile  | 18 +++++-------------
 biology/stacks/distinfo  |  6 +++---
 biology/stacks/pkg-plist |  6 ++++--
 3 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile
index b4301eec2bb7..5e1b270e1b98 100644
--- a/biology/stacks/Makefile
+++ b/biology/stacks/Makefile
@@ -1,8 +1,7 @@
 PORTNAME=	stacks
-DISTVERSION=	2.4
-PORTREVISION=	2
+DISTVERSION=	2.68
 CATEGORIES=	biology perl5 python
-MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+MASTER_SITES=	https://catchenlab.life.illinois.edu/stacks/source/
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Software pipeline for building loci from short-read sequences
@@ -13,17 +12,10 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		compiler:c++11-lang gmake python shebangfix
 
-SHEBANG_FILES=	scripts/*.pl scripts/*.py \
-		scripts/stacks-integrate-alignments scripts/stacks-gdb
+SHEBANG_FILES=	scripts/*
+
 GNU_CONFIGURE=	yes
 
 LDFLAGS+=	-lpthread
 
-.include <bsd.port.pre.mk>
-
-# Temp workaround, see PR 230888
-.if ${ARCH} == i386
-USE_GCC=	yes
-.endif
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo
index 312ef425ec9d..ce462d89a52e 100644
--- a/biology/stacks/distinfo
+++ b/biology/stacks/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557519159
-SHA256 (stacks-2.4.tar.gz) = 30093d688a2dc62a19ea42a58065f024c8279419439049bcde186703e75641c1
-SIZE (stacks-2.4.tar.gz) = 10930616
+TIMESTAMP = 1733920483
+SHA256 (stacks-2.68.tar.gz) = 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650
+SIZE (stacks-2.68.tar.gz) = 15552836
diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist
index 605cf4a295db..e3ca8c4a9b60 100644
--- a/biology/stacks/pkg-plist
+++ b/biology/stacks/pkg-plist
@@ -1,9 +1,7 @@
 bin/clone_filter
-bin/count_fixed_catalog_snps.py
 bin/cstacks
 bin/denovo_map.pl
 bin/gstacks
-bin/integrate_alignments.py
 bin/kmer_filter
 bin/phasedstacks
 bin/populations
@@ -11,8 +9,12 @@ bin/process_radtags
 bin/process_shortreads
 bin/ref_map.pl
 bin/sstacks
+bin/stacks-count-reads-per-sample-per-locus
 bin/stacks-dist-extract
 bin/stacks-gdb
+bin/stacks-hist2d-loci-samples-coverage
 bin/stacks-integrate-alignments
+bin/stacks-private-alleles
+bin/stacks-samtools-tview
 bin/tsv2bam
 bin/ustacks