[pkgsrc/trunk]: pkgsrc/biology/stacks biology/stacks: Update to 2.60

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/0350b98b070a
branches:  trunk
changeset: 375624:0350b98b070a
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Thu Mar 17 23:49:08 2022 +0000

description:
biology/stacks: Update to 2.60

Numerous bug fixes and enhancements since 2.2
Unbreak build on Darwin

diffstat:

 biology/stacks/Makefile |  36 ++++++++++++++++++++++++--------
 biology/stacks/PLIST    |  54 +++---------------------------------------------
 biology/stacks/distinfo |   8 +++---
 3 files changed, 35 insertions(+), 63 deletions(-)

diffs (143 lines):

diff -r 5c9d90331a02 -r 0350b98b070a biology/stacks/Makefile
--- a/biology/stacks/Makefile   Thu Mar 17 22:23:23 2022 +0000
+++ b/biology/stacks/Makefile   Thu Mar 17 23:49:08 2022 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.6 2021/05/24 19:49:12 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2022/03/17 23:49:08 bacon Exp $
 
-DISTNAME=      stacks-2.2
-PKGREVISION=   5
+DISTNAME=      stacks-2.60
 CATEGORIES=    biology
 MASTER_SITES=  http://catchenlab.life.illinois.edu/stacks/source/
 
@@ -11,17 +10,36 @@
 LICENSE=       gnu-gpl-v2
 
 USE_LANGUAGES= c c++14
-GCC_REQD+=     4.9
 USE_TOOLS+=    bash perl:run
 GNU_CONFIGURE= yes
 
-REPLACE_BASH=  scripts/stacks-integrate-alignments scripts/stacks-gdb
-REPLACE_BASH+= scripts/stacks-dist-extract
-REPLACE_PERL=  scripts/*.pl
-REPLACE_PYTHON=        scripts/*.py
+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-integrate-alignments
+
+REPLACE_INTERPRETER+=  Rscript
+REPLACE.Rscript.old=   .*Rscript
+REPLACE.Rscript.new=   ${PREFIX}/bin/Rscript
+REPLACE_FILES.Rscript= scripts/stacks-hist2d-loci-samples-coverage
 
-CFLAGS+=       -fopenmp
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == Darwin
+# pkgsrc sed wrapper lacks -i
+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|'
+.else
+# macOS clang lacks OpenMP
+CFLAGS+=               -fopenmp
+.endif
 
 .include "../../lang/python/application.mk"
+.include "../../math/R/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 5c9d90331a02 -r 0350b98b070a biology/stacks/PLIST
--- a/biology/stacks/PLIST      Thu Mar 17 22:23:23 2022 +0000
+++ b/biology/stacks/PLIST      Thu Mar 17 23:49:08 2022 +0000
@@ -1,10 +1,8 @@
-@comment $NetBSD: PLIST,v 1.1 2018/12/22 21:52:06 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2022/03/17 23:49:08 bacon Exp $
 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
@@ -12,55 +10,11 @@
 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-samtools-tview
 bin/tsv2bam
 bin/ustacks
-share/stacks/php/CatalogClass.php
-share/stacks/php/Locus.php
-share/stacks/php/ajax.js
-share/stacks/php/annotate.js
-share/stacks/php/annotate_marker.php
-share/stacks/php/catalog.php
-share/stacks/php/catalog_genotypes.php
-share/stacks/php/constants.php.dist
-share/stacks/php/correct_genotype.php
-share/stacks/php/correct_genotypes.php
-share/stacks/php/db_functions.php
-share/stacks/php/export.js
-share/stacks/php/export_batch.php
-share/stacks/php/fst_view.php
-share/stacks/php/hapstat_view.php
-share/stacks/php/header.php
-share/stacks/php/images/caret-d.png
-share/stacks/php/images/caret-u.png
-share/stacks/php/images/excel_icon.png
-share/stacks/php/images/l-arrow-disabled.png
-share/stacks/php/images/l-arrow.png
-share/stacks/php/images/r-arrow-disabled.png
-share/stacks/php/images/r-arrow.png
-share/stacks/php/images/stacks_bg.png
-share/stacks/php/images/stacks_logo_rev_small.png
-share/stacks/php/index.php
-share/stacks/php/last_modified.php
-share/stacks/php/phist_view.php
-share/stacks/php/pop_view.php
-share/stacks/php/population_view.js
-share/stacks/php/samples.php
-share/stacks/php/sequence_blast.php
-share/stacks/php/stack_view.php
-share/stacks/php/stacks.css
-share/stacks/php/stacks.js
-share/stacks/php/stacks_functions.php
-share/stacks/php/sumstat_view.php
-share/stacks/php/tag.php
-share/stacks/php/tags.php
-share/stacks/php/version.php
-share/stacks/php/view_sequence.php
-share/stacks/sql/catalog_index.sql
-share/stacks/sql/chr_index.sql
-share/stacks/sql/mysql.cnf.dist
-share/stacks/sql/stacks.sql
-share/stacks/sql/tag_index.sql
-@pkgdir share/stacks/php/export
diff -r 5c9d90331a02 -r 0350b98b070a biology/stacks/distinfo
--- a/biology/stacks/distinfo   Thu Mar 17 22:23:23 2022 +0000
+++ b/biology/stacks/distinfo   Thu Mar 17 23:49:08 2022 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:44 nia Exp $
+$NetBSD: distinfo,v 1.4 2022/03/17 23:49:08 bacon Exp $
 
-BLAKE2s (stacks-2.2.tar.gz) = d5b6c2353e4888abfe9a721552718bd76d5705cd94209f7af0fafac37bd70bf3
-SHA512 (stacks-2.2.tar.gz) = f1cffd12313fed1c171af46f9fb501373b43d57cd3004edae1034074f43169d43398743cf625ffa21be412c808ba1168513a33c63377ee13dd056406fa222095
-Size (stacks-2.2.tar.gz) = 10822973 bytes
+BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
+SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
+Size (stacks-2.60.tar.gz) = 12135281 bytes