stacks: Update to 2.68

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <jtocino%gmx.com@localhost>
Pushed By:	outpaddling
Date:		Thu Jan 16 18:04:22 2025 -0600
Changeset:	f53a4ca1db7d59e413ae947d34a09e843ed3b230

Modified Files:
	stacks/Makefile
	stacks/PLIST
	stacks/distinfo

Log Message:
stacks: Update to 2.68

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f53a4ca1db7d59e413ae947d34a09e843ed3b230

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 stacks/Makefile | 10 +++++++---
 stacks/PLIST    |  3 ++-
 stacks/distinfo |  8 ++++----
 3 files changed, 13 insertions(+), 8 deletions(-)

diffs:
diff --git a/stacks/Makefile b/stacks/Makefile
index 2dfa19f0d3..1c2eaa0656 100644
--- a/stacks/Makefile
+++ b/stacks/Makefile
@@ -1,7 +1,6 @@
 # $NetBSD: Makefile,v 1.11 2023/08/14 05:23:52 wiz Exp $
 
-DISTNAME=	stacks-2.60
-PKGREVISION=	3
+DISTNAME=	stacks-2.68
 CATEGORIES=	biology
 MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
 
@@ -12,16 +11,21 @@ LICENSE=	gnu-gpl-v2
 
 USE_LANGUAGES=		c c++
 USE_CXX_FEATURES=	c++14
+# Is this needed?
+# FORCE_CXX_STD=	c++14
 USE_TOOLS+=		bash perl:run
 GNU_CONFIGURE=		yes
 
 REPLACE_BASH+=		scripts/stacks-count-reads-per-sample-per-locus
-REPLACE_BASH+=		scripts/stacks-dist-extract
 REPLACE_BASH+=		scripts/stacks-gdb
 REPLACE_BASH+=		scripts/stacks-samtools-tview
 REPLACE_PERL=		scripts/*.pl
 REPLACE_PYTHON+=	scripts/*.py
+REPLACE_PYTHON+=	scripts/stacks-dist-extract
 REPLACE_PYTHON+=	scripts/stacks-integrate-alignments
+REPLACE_PYTHON+=	scripts/stacks-private-alleles
+
+ERROR: [check-interpreter.mk] The interpreter "/usr/bin/env" of "/home/bacon/Pkgsrc/pkgsrc/wip/stacks/work/.destdir/home/bacon/Pkgsrc/pkg/bin/stacks-private-alleles" is not allowed.
 
 REPLACE_INTERPRETER+=	Rscript
 REPLACE.Rscript.old=	.*Rscript
diff --git a/stacks/PLIST b/stacks/PLIST
index 80a6f82831..4deba5bdc3 100644
--- a/stacks/PLIST
+++ b/stacks/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2022/03/17 23:49:08 bacon Exp $
+@comment $NetBSD$
 bin/clone_filter
 bin/cstacks
 bin/denovo_map.pl
@@ -15,6 +15,7 @@ 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
diff --git a/stacks/distinfo b/stacks/distinfo
index cb3192c697..d9b8cbe34d 100644
--- a/stacks/distinfo
+++ b/stacks/distinfo
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.5 2022/04/25 14:34:06 tnn Exp $
+$NetBSD$
 
-BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
-SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
-Size (stacks-2.60.tar.gz) = 12135281 bytes
+BLAKE2s (stacks-2.68.tar.gz) = 149419fb6ca34333aa1850e44e18054c0a1aa45564a88cfba542142f5581f79c
+SHA512 (stacks-2.68.tar.gz) = 32ec2fc8c493128ec0a9aca0dced64cde485014a9236e80959c8a10a69b7d970f216c564c91d5fdc0773ad0ed0e6dce2c581ddd709788ed044a053f62cc2b1b0
+Size (stacks-2.68.tar.gz) = 15552836 bytes
 SHA1 (patch-src_Hwp.cc) = 15b1872fd0199a13020cecf7ff34478cf83007fd
 SHA1 (patch-src_PopSum.cc) = fbf56bbdb3f8e0cc146ca19c75c910fbc00ae36b
 SHA1 (patch-src_Vcf.cc) = 26f04decced076cd189fe3162c4641809d070060