Thu Mar 17 23:49:08 2022 UTC ()
biology/stacks: Update to 2.60

Numerous bug fixes and enhancements since 2.2
Unbreak build on Darwin


(bacon)
diff -r1.6 -r1.7 pkgsrc/biology/stacks/Makefile
diff -r1.1 -r1.2 pkgsrc/biology/stacks/PLIST
diff -r1.3 -r1.4 pkgsrc/biology/stacks/distinfo
cvs diff -r1.6 -r1.7 pkgsrc/biology/stacks/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/stacks/Makefile 2021/05/24 19:49:12 1.6
+++ pkgsrc/biology/stacks/Makefile 2022/03/17 23:49:08 1.7
@@ -1,27 +1,45 @@ @@ -1,27 +1,45 @@
1# $NetBSD: Makefile,v 1.6 2021/05/24 19:49:12 wiz Exp $ 1# $NetBSD: Makefile,v 1.7 2022/03/17 23:49:08 bacon Exp $
2 2
3DISTNAME= stacks-2.2 3DISTNAME= stacks-2.60
4PKGREVISION= 5 
5CATEGORIES= biology 4CATEGORIES= biology
6MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ 5MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/
7 6
8MAINTAINER= bacon@NetBSD.org 7MAINTAINER= bacon@NetBSD.org
9HOMEPAGE= http://catchenlab.life.illinois.edu/stacks/ 8HOMEPAGE= http://catchenlab.life.illinois.edu/stacks/
10COMMENT= Software pipeline for building loci from short-read sequences 9COMMENT= Software pipeline for building loci from short-read sequences
11LICENSE= gnu-gpl-v2 10LICENSE= gnu-gpl-v2
12 11
13USE_LANGUAGES= c c++14 12USE_LANGUAGES= c c++14
14GCC_REQD+= 4.9 
15USE_TOOLS+= bash perl:run 13USE_TOOLS+= bash perl:run
16GNU_CONFIGURE= yes 14GNU_CONFIGURE= yes
17 15
18REPLACE_BASH= scripts/stacks-integrate-alignments scripts/stacks-gdb 16REPLACE_BASH+= scripts/stacks-count-reads-per-sample-per-locus
19REPLACE_BASH+= scripts/stacks-dist-extract 17REPLACE_BASH+= scripts/stacks-dist-extract
20REPLACE_PERL= scripts/*.pl 18REPLACE_BASH+= scripts/stacks-gdb
21REPLACE_PYTHON= scripts/*.py 19REPLACE_BASH+= scripts/stacks-samtools-tview
22 20REPLACE_PERL= scripts/*.pl
23CFLAGS+= -fopenmp 21REPLACE_PYTHON+= scripts/*.py
 22REPLACE_PYTHON+= scripts/stacks-integrate-alignments
 23
 24REPLACE_INTERPRETER+= Rscript
 25REPLACE.Rscript.old= .*Rscript
 26REPLACE.Rscript.new= ${PREFIX}/bin/Rscript
 27REPLACE_FILES.Rscript= scripts/stacks-hist2d-loci-samples-coverage
 28
 29.include "../../mk/bsd.prefs.mk"
 30
 31.if ${OPSYS} == Darwin
 32# pkgsrc sed wrapper lacks -i
 33SUBST_CLASSES+= sed
 34SUBST_STAGE.sed= pre-configure
 35SUBST_FILES.sed= Makefile.in
 36SUBST_SED.sed= -e 's|sed -i.bkp|/usr/bin/sed -i .bkp|'
 37.else
 38# macOS clang lacks OpenMP
 39CFLAGS+= -fopenmp
 40.endif
24 41
25.include "../../lang/python/application.mk" 42.include "../../lang/python/application.mk"
 43.include "../../math/R/buildlink3.mk"
26.include "../../devel/zlib/buildlink3.mk" 44.include "../../devel/zlib/buildlink3.mk"
27.include "../../mk/bsd.pkg.mk" 45.include "../../mk/bsd.pkg.mk"
cvs diff -r1.1 -r1.2 pkgsrc/biology/stacks/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/stacks/PLIST 2018/12/22 21:52:06 1.1
+++ pkgsrc/biology/stacks/PLIST 2022/03/17 23:49:08 1.2
@@ -1,66 +1,20 @@ @@ -1,66 +1,20 @@
1@comment $NetBSD: PLIST,v 1.1 2018/12/22 21:52:06 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.2 2022/03/17 23:49:08 bacon Exp $
2bin/clone_filter 2bin/clone_filter
3bin/count_fixed_catalog_snps.py 
4bin/cstacks 3bin/cstacks
5bin/denovo_map.pl 4bin/denovo_map.pl
6bin/gstacks 5bin/gstacks
7bin/integrate_alignments.py 
8bin/kmer_filter 6bin/kmer_filter
9bin/phasedstacks 7bin/phasedstacks
10bin/populations 8bin/populations
11bin/process_radtags 9bin/process_radtags
12bin/process_shortreads 10bin/process_shortreads
13bin/ref_map.pl 11bin/ref_map.pl
14bin/sstacks 12bin/sstacks
 13bin/stacks-count-reads-per-sample-per-locus
15bin/stacks-dist-extract 14bin/stacks-dist-extract
16bin/stacks-gdb 15bin/stacks-gdb
 16bin/stacks-hist2d-loci-samples-coverage
17bin/stacks-integrate-alignments 17bin/stacks-integrate-alignments
 18bin/stacks-samtools-tview
18bin/tsv2bam 19bin/tsv2bam
19bin/ustacks 20bin/ustacks
20share/stacks/php/CatalogClass.php 
21share/stacks/php/Locus.php 
22share/stacks/php/ajax.js 
23share/stacks/php/annotate.js 
24share/stacks/php/annotate_marker.php 
25share/stacks/php/catalog.php 
26share/stacks/php/catalog_genotypes.php 
27share/stacks/php/constants.php.dist 
28share/stacks/php/correct_genotype.php 
29share/stacks/php/correct_genotypes.php 
30share/stacks/php/db_functions.php 
31share/stacks/php/export.js 
32share/stacks/php/export_batch.php 
33share/stacks/php/fst_view.php 
34share/stacks/php/hapstat_view.php 
35share/stacks/php/header.php 
36share/stacks/php/images/caret-d.png 
37share/stacks/php/images/caret-u.png 
38share/stacks/php/images/excel_icon.png 
39share/stacks/php/images/l-arrow-disabled.png 
40share/stacks/php/images/l-arrow.png 
41share/stacks/php/images/r-arrow-disabled.png 
42share/stacks/php/images/r-arrow.png 
43share/stacks/php/images/stacks_bg.png 
44share/stacks/php/images/stacks_logo_rev_small.png 
45share/stacks/php/index.php 
46share/stacks/php/last_modified.php 
47share/stacks/php/phist_view.php 
48share/stacks/php/pop_view.php 
49share/stacks/php/population_view.js 
50share/stacks/php/samples.php 
51share/stacks/php/sequence_blast.php 
52share/stacks/php/stack_view.php 
53share/stacks/php/stacks.css 
54share/stacks/php/stacks.js 
55share/stacks/php/stacks_functions.php 
56share/stacks/php/sumstat_view.php 
57share/stacks/php/tag.php 
58share/stacks/php/tags.php 
59share/stacks/php/version.php 
60share/stacks/php/view_sequence.php 
61share/stacks/sql/catalog_index.sql 
62share/stacks/sql/chr_index.sql 
63share/stacks/sql/mysql.cnf.dist 
64share/stacks/sql/stacks.sql 
65share/stacks/sql/tag_index.sql 
66@pkgdir share/stacks/php/export 
cvs diff -r1.3 -r1.4 pkgsrc/biology/stacks/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/stacks/distinfo 2021/10/26 10:03:44 1.3
+++ pkgsrc/biology/stacks/distinfo 2022/03/17 23:49:08 1.4
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
1$NetBSD: distinfo,v 1.3 2021/10/26 10:03:44 nia Exp $ 1$NetBSD: distinfo,v 1.4 2022/03/17 23:49:08 bacon Exp $
2 2
3BLAKE2s (stacks-2.2.tar.gz) = d5b6c2353e4888abfe9a721552718bd76d5705cd94209f7af0fafac37bd70bf3 3BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
4SHA512 (stacks-2.2.tar.gz) = f1cffd12313fed1c171af46f9fb501373b43d57cd3004edae1034074f43169d43398743cf625ffa21be412c808ba1168513a33c63377ee13dd056406fa222095 4SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
5Size (stacks-2.2.tar.gz) = 10822973 bytes 5Size (stacks-2.60.tar.gz) = 12135281 bytes