stacks: Restore deleted package

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: stacks: Restore deleted package
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 19 May 2023 12:05:22 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri May 19 07:05:22 2023 -0500
Changeset:	d30efd1813de9e0e25da7e869f110c1c6437f373

Added Files:
	stacks/DESCR
	stacks/Makefile
	stacks/PLIST
	stacks/distinfo
	stacks/patches/patch-src_Hwp.cc
	stacks/patches/patch-src_PopSum.cc
	stacks/patches/patch-src_Vcf.cc
	stacks/patches/patch-src_kmers.cc
	stacks/patches/patch-src_smoothing__utils.h
	stacks/patches/patch-src_utils.cc

Log Message:
stacks: Restore deleted package

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d30efd1813de9e0e25da7e869f110c1c6437f373

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

diffstat:
 stacks/DESCR                                |  4 +++
 stacks/Makefile                             | 48 +++++++++++++++++++++++++++++
 stacks/PLIST                                | 20 ++++++++++++
 stacks/distinfo                             | 11 +++++++
 stacks/patches/patch-src_Hwp.cc             | 16 ++++++++++
 stacks/patches/patch-src_PopSum.cc          | 15 +++++++++
 stacks/patches/patch-src_Vcf.cc             | 15 +++++++++
 stacks/patches/patch-src_kmers.cc           | 16 ++++++++++
 stacks/patches/patch-src_smoothing__utils.h | 15 +++++++++
 stacks/patches/patch-src_utils.cc           | 16 ++++++++++
 10 files changed, 176 insertions(+)

diffs:
diff --git a/stacks/DESCR b/stacks/DESCR
new file mode 100644
index 0000000000..91c14fbc8d
--- /dev/null
+++ b/stacks/DESCR
@@ -0,0 +1,4 @@
+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.
diff --git a/stacks/Makefile b/stacks/Makefile
new file mode 100644
index 0000000000..27d74bf8d7
--- /dev/null
+++ b/stacks/Makefile
@@ -0,0 +1,48 @@
+# $NetBSD: Makefile,v 1.10 2022/06/30 11:18:05 nia Exp $
+
+DISTNAME=	stacks-2.60
+PKGREVISION=	2
+CATEGORIES=	biology
+MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://catchenlab.life.illinois.edu/stacks/
+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
+
+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
+
+.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
+
+LDFLAGS.SunOS+=		-lsocket
+
+.include "../../lang/python/application.mk"
+.include "../../math/R/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/stacks/PLIST b/stacks/PLIST
new file mode 100644
index 0000000000..80a6f82831
--- /dev/null
+++ b/stacks/PLIST
@@ -0,0 +1,20 @@
+@comment $NetBSD: PLIST,v 1.2 2022/03/17 23:49:08 bacon Exp $
+bin/clone_filter
+bin/cstacks
+bin/denovo_map.pl
+bin/gstacks
+bin/kmer_filter
+bin/phasedstacks
+bin/populations
+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-samtools-tview
+bin/tsv2bam
+bin/ustacks
diff --git a/stacks/distinfo b/stacks/distinfo
new file mode 100644
index 0000000000..cb3192c697
--- /dev/null
+++ b/stacks/distinfo
@@ -0,0 +1,11 @@
+$NetBSD: distinfo,v 1.5 2022/04/25 14:34:06 tnn Exp $
+
+BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
+SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
+Size (stacks-2.60.tar.gz) = 12135281 bytes
+SHA1 (patch-src_Hwp.cc) = 15b1872fd0199a13020cecf7ff34478cf83007fd
+SHA1 (patch-src_PopSum.cc) = fbf56bbdb3f8e0cc146ca19c75c910fbc00ae36b
+SHA1 (patch-src_Vcf.cc) = 26f04decced076cd189fe3162c4641809d070060
+SHA1 (patch-src_kmers.cc) = 8fbe6c7be1d35f4dc17f2f250538c9b5f136e524
+SHA1 (patch-src_smoothing__utils.h) = be331ef1d89998b946cf923d95f9eda676a245ab
+SHA1 (patch-src_utils.cc) = 3474a1d0dcc395892e362c877df0daa33050b500
diff --git a/stacks/patches/patch-src_Hwp.cc b/stacks/patches/patch-src_Hwp.cc
new file mode 100644
index 0000000000..49b1954fee
--- /dev/null
+++ b/stacks/patches/patch-src_Hwp.cc
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_Hwp.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/Hwp.cc.orig	2020-06-24 17:47:53.000000000 +0000
++++ src/Hwp.cc
+@@ -20,6 +20,9 @@
+ 
+ #include "Hwp.h"
+ 
++using std::log;
++using std::pow;
++
+ double
+ GuoThompson_Hwp::exec_locus(int start, int end, const Datum **d, size_t hap_cnt)
+ {
diff --git a/stacks/patches/patch-src_PopSum.cc b/stacks/patches/patch-src_PopSum.cc
new file mode 100644
index 0000000000..47be3273ff
--- /dev/null
+++ b/stacks/patches/patch-src_PopSum.cc
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_PopSum.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/PopSum.cc.orig	2021-10-21 14:47:59.000000000 +0000
++++ src/PopSum.cc
+@@ -20,6 +20,8 @@
+ 
+ #include "PopSum.h"
+ 
++using std::log;
++
+ LocPopSum::LocPopSum(size_t cloc_len, const MetaPopInfo& mpopi)
+ {
+     this->_pop_cnt  = mpopi.pops().size();
diff --git a/stacks/patches/patch-src_Vcf.cc b/stacks/patches/patch-src_Vcf.cc
new file mode 100644
index 0000000000..519f1bdebf
--- /dev/null
+++ b/stacks/patches/patch-src_Vcf.cc
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_Vcf.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/Vcf.cc.orig	2021-06-28 20:21:30.000000000 +0000
++++ src/Vcf.cc
+@@ -22,6 +22,8 @@
+ 
+ #include "Vcf.h"
+ 
++using std::log;
++
+ const VcfMeta VcfMeta::predefs::info_AD ("INFO","<ID=AD,Number=R,Type=Integer,Description=\"Total Depth for Each Allele\">");
+ const VcfMeta VcfMeta::predefs::info_AF ("INFO","<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">");
+ const VcfMeta VcfMeta::predefs::info_DP ("INFO","<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
diff --git a/stacks/patches/patch-src_kmers.cc b/stacks/patches/patch-src_kmers.cc
new file mode 100644
index 0000000000..e5999c5763
--- /dev/null
+++ b/stacks/patches/patch-src_kmers.cc
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_kmers.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/kmers.cc.orig	2021-06-08 21:08:14.000000000 +0000
++++ src/kmers.cc
+@@ -23,6 +23,9 @@
+ //
+ #include "kmers.h"
+ 
++using std::floor;
++using std::pow;
++
+ int determine_kmer_length(int read_len, int dist) {
+     int kmer_len, span, min_matches;
+ 
diff --git a/stacks/patches/patch-src_smoothing__utils.h b/stacks/patches/patch-src_smoothing__utils.h
new file mode 100644
index 0000000000..87fba3ab29
--- /dev/null
+++ b/stacks/patches/patch-src_smoothing__utils.h
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_smoothing__utils.h,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/smoothing_utils.h.orig	2020-06-24 17:47:55.000000000 +0000
++++ src/smoothing_utils.h
+@@ -24,6 +24,8 @@
+ #include <cmath>
+ #include <vector>
+ 
++using std::pow;
++
+ extern double sigma;
+ 
+ inline
diff --git a/stacks/patches/patch-src_utils.cc b/stacks/patches/patch-src_utils.cc
new file mode 100644
index 0000000000..bd1f0979e7
--- /dev/null
+++ b/stacks/patches/patch-src_utils.cc
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_utils.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+provide fallback declaration for ACCESSPERMS
+
+--- src/utils.cc.orig	2021-10-07 19:33:41.000000000 +0000
++++ src/utils.cc
+@@ -401,6 +401,9 @@ void check_or_mk_dir(const string& path)
+             cerr << "Error: '" << *path_p << "' is not a directory.\n";
+             throw exception();
+         }
++#ifndef ACCESSPERMS
++#define ACCESSPERMS (S_IRWXU|S_IRWXG|S_IRWXO)
++#endif
+     } else if (mkdir(path_p->c_str(), ACCESSPERMS) != 0) {
+         //
+         // Failed to create the directory.
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