CVS commit: pkgsrc/biology/stacks

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Jan 18 13:52:23 UTC 2025

Modified Files:
        pkgsrc/biology/stacks: DESCR Makefile PLIST distinfo

Log Message:
biology/stacks: Update to 2.68

Numerous fixes and improvements since 2.6
Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/stacks/DESCR
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/stacks/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/stacks/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/stacks/distinfo

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

Modified files:

Index: pkgsrc/biology/stacks/DESCR
diff -u pkgsrc/biology/stacks/DESCR:1.1 pkgsrc/biology/stacks/DESCR:1.2
--- pkgsrc/biology/stacks/DESCR:1.1     Sat Dec 22 21:52:06 2018
+++ pkgsrc/biology/stacks/DESCR Sat Jan 18 13:52:23 2025
@@ -1,4 +1,5 @@
-Stacks is a software pipeline for building loci from short-read sequences, such
-as those generated on the Illumina platform. Stacks was developed to work with
-restriction enzyme-based data, such as RAD-seq, for the purpose of building
-genetic maps and conducting population genomics and phylogeography.
+Stacks is a software pipeline for building loci from short-read
+sequences, such as those generated on the Illumina platform. Stacks
+was developed to work with restriction enzyme-based data, such as
+RAD-seq, for the purpose of building genetic maps and conducting
+population genomics and phylogeography.

Index: pkgsrc/biology/stacks/Makefile
diff -u pkgsrc/biology/stacks/Makefile:1.11 pkgsrc/biology/stacks/Makefile:1.12
--- pkgsrc/biology/stacks/Makefile:1.11 Mon Aug 14 05:23:52 2023
+++ pkgsrc/biology/stacks/Makefile      Sat Jan 18 13:52:23 2025
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.11 2023/08/14 05:23:52 wiz Exp $
+# $NetBSD: Makefile,v 1.12 2025/01/18 13:52:23 bacon Exp $
 
-DISTNAME=      stacks-2.60
-PKGREVISION=   3
+DISTNAME=      stacks-2.68
 CATEGORIES=    biology
 MASTER_SITES=  http://catchenlab.life.illinois.edu/stacks/source/
 
@@ -10,17 +9,19 @@ HOMEPAGE=    http://catchenlab.life.illinoi
 COMMENT=       Software pipeline for building loci from short-read sequences
 LICENSE=       gnu-gpl-v2
 
-USE_LANGUAGES= c c++14
-USE_TOOLS+=    bash perl:run
-GNU_CONFIGURE= yes
+USE_LANGUAGES=         c c++
+USE_CXX_FEATURES=      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
 
 REPLACE_INTERPRETER+=  Rscript
 REPLACE.Rscript.old=   .*Rscript
@@ -35,6 +36,9 @@ SUBST_CLASSES+=               sed
 SUBST_STAGE.sed=       pre-configure
 SUBST_FILES.sed=       Makefile.in
 SUBST_SED.sed=         -e 's|sed -i.bkp|/usr/bin/sed -i .bkp|'
+CFLAGS+=               -Xpreprocessor -fopenmp
+
+.include "../../parallel/openmp/buildlink3.mk"
 .else
 # macOS clang lacks OpenMP
 CFLAGS+=               -fopenmp

Index: pkgsrc/biology/stacks/PLIST
diff -u pkgsrc/biology/stacks/PLIST:1.2 pkgsrc/biology/stacks/PLIST:1.3
--- pkgsrc/biology/stacks/PLIST:1.2     Thu Mar 17 23:49:08 2022
+++ pkgsrc/biology/stacks/PLIST Sat Jan 18 13:52:23 2025
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2022/03/17 23:49:08 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2025/01/18 13:52:23 bacon Exp $
 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

Index: pkgsrc/biology/stacks/distinfo
diff -u pkgsrc/biology/stacks/distinfo:1.5 pkgsrc/biology/stacks/distinfo:1.6
--- pkgsrc/biology/stacks/distinfo:1.5  Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/distinfo      Sat Jan 18 13:52:23 2025
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.5 2022/04/25 14:34:06 tnn Exp $
+$NetBSD: distinfo,v 1.6 2025/01/18 13:52:23 bacon Exp $
 
-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