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haplohseq: Resurrect and begin updates for boost 1.86+



Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <jtocino%gmx.com@localhost>
Pushed By:	outpaddling
Date:		Sun Jan 26 07:55:28 2025 -0600
Changeset:	a85659bf6f3111440d51a9180f9c44acb2d3c3b9

Modified Files:
	Makefile
Added Files:
	haplohseq/DESCR
	haplohseq/Makefile
	haplohseq/PLIST
	haplohseq/distinfo
	haplohseq/files/haplohseq-example.in
	haplohseq/patches/patch-src_HaplohSeq.cpp

Log Message:
haplohseq: Resurrect and begin updates for boost 1.86+

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a85659bf6f3111440d51a9180f9c44acb2d3c3b9

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

diffstat:
 Makefile                                  |  1 +
 haplohseq/DESCR                           |  5 +++
 haplohseq/Makefile                        | 44 +++++++++++++++++++++++
 haplohseq/PLIST                           |  9 +++++
 haplohseq/distinfo                        |  6 ++++
 haplohseq/files/haplohseq-example.in      | 37 +++++++++++++++++++
 haplohseq/patches/patch-src_HaplohSeq.cpp | 60 +++++++++++++++++++++++++++++++
 7 files changed, 162 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 7fd5582efb..ce204ff180 100644
--- a/Makefile
+++ b/Makefile
@@ -1474,6 +1474,7 @@ SUBDIR+=	halfempty
 SUBDIR+=	halloy
 SUBDIR+=	hammer
 SUBDIR+=	hanazono-ttf
+SUBDIR+=	haplhoseq
 SUBDIR+=	hare
 SUBDIR+=	harec
 SUBDIR+=	harmony
diff --git a/haplohseq/DESCR b/haplohseq/DESCR
new file mode 100644
index 0000000000..0b2c07f64d
--- /dev/null
+++ b/haplohseq/DESCR
@@ -0,0 +1,5 @@
+Haplohseq identifies regions of allelic imbalance (AI) in sequencing
+data obtained from impure samples where AI events exist in a
+potentially low proportion of cells in the sample.  Input to the
+software includes a VCF file of genotypes and estimated phased
+genotypes.
diff --git a/haplohseq/Makefile b/haplohseq/Makefile
new file mode 100644
index 0000000000..d38916d05d
--- /dev/null
+++ b/haplohseq/Makefile
@@ -0,0 +1,44 @@
+# $NetBSD: Makefile,v 1.3 2024/12/29 15:09:39 adam Exp $
+
+DISTNAME=	haplohseq-0.1.2.2
+PKGREVISION=	2
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_PROJECT=	haplohseq
+GITHUB_TAG=	e4892945eced075a5bb98f208786cdf85eb3d82a
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+COMMENT=	Identify regions of allelic imbalance
+LICENSE=	mit
+
+SUBST_CLASSES+=		test
+SUBST_STAGE.test=	pre-configure
+SUBST_SED.test=		-e 's|\.\./haplohseq|haplohseq|'
+SUBST_SED.test+=	-e 's|python|${PYTHONBIN}|'
+SUBST_FILES.test=	example/example_run.sh
+
+USE_LANGUAGES=		c c++
+USE_CXX_FEATURES+=	c++14	# Minimum for boost, maximum for haplohseq
+FORCE_CXX_STD+=		c++14
+USE_TOOLS+=		gmake pax
+MAKE_FILE=		makefile
+
+EXAMPLESDIR=	${PREFIX}/share/examples/haplohseq
+
+INSTALLATION_DIRS=	share/examples/haplohseq
+
+post-patch:
+	${SED} -e "s|%%EXAMPLESDIR%%|${EXAMPLESDIR}|" \
+		${FILESDIR}/haplohseq-example.in > ${WRKDIR}/haplohseq-example
+
+post-install:
+	${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${DESTDIR}${PREFIX}/bin
+	(cd ${WRKSRC} && pax -rw example ldmap scripts ${DESTDIR}${EXAMPLESDIR})
+
+do-test:
+	(cd ${WRKSRC}/build/test && ${SH} ${WRKSRC}/src/test/run-tests)
+
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/haplohseq/PLIST b/haplohseq/PLIST
new file mode 100644
index 0000000000..9737854f81
--- /dev/null
+++ b/haplohseq/PLIST
@@ -0,0 +1,9 @@
+@comment $NetBSD: PLIST,v 1.1 2024/10/12 12:19:51 bacon Exp $
+bin/haplohseq
+bin/haplohseq-example
+share/examples/haplohseq/example/example_input/tumor_exome.vcf
+share/examples/haplohseq/example/example_run.sh
+share/examples/haplohseq/ldmap/hg19.exome.ldmap
+share/examples/haplohseq/scripts/haplohseq_plot.R
+share/examples/haplohseq/scripts/ldmap.py
+share/examples/haplohseq/scripts/simple_phaser.py
diff --git a/haplohseq/distinfo b/haplohseq/distinfo
new file mode 100644
index 0000000000..a6071e47fd
--- /dev/null
+++ b/haplohseq/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2024/10/12 12:19:51 bacon Exp $
+
+BLAKE2s (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = dbd48a3854197dbf71189a56bdd0075ce8e6a78bca92b58673ae2770eae3daa6
+SHA512 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 8de2c75d4e443eab79f520d43bd2e0c238dca798bf53cc7821d6fe8bdf94f3d3ae3b9319b9b21aae10dab6b52e5c1e81380380c456a240bfcfa8863b83c5feff
+Size (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 12085199 bytes
+SHA1 (patch-src_HaplohSeq.cpp) = 9907808c0cb1f353f7c9784fd22def84e77a2a9d
diff --git a/haplohseq/files/haplohseq-example.in b/haplohseq/files/haplohseq-example.in
new file mode 100644
index 0000000000..0cb2a5bee1
--- /dev/null
+++ b/haplohseq/files/haplohseq-example.in
@@ -0,0 +1,37 @@
+#!/bin/sh -e
+
+##########################################################################
+#   Script description:
+#       Run haplohseq example
+#
+#   https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+#       
+#   History:
+#   Date        Name        Modification
+#   2019-11-13  Jason Bacon Begin
+##########################################################################
+
+usage()
+{
+    printf "Usage: $0 directory\n"
+    exit 1
+}
+
+
+##########################################################################
+#   Main
+##########################################################################
+
+if [ $# != 1 ]; then
+    usage
+fi
+
+dir="$1"
+
+if [ -e "$dir" ]; then
+    printf "'$dir' already exists.  Please remove it or specify another.\n"
+    exit 1
+fi
+cp -R %%EXAMPLESDIR%% "$dir"
+cd "$dir/example"
+sh ./example_run.sh
diff --git a/haplohseq/patches/patch-src_HaplohSeq.cpp b/haplohseq/patches/patch-src_HaplohSeq.cpp
new file mode 100644
index 0000000000..c2b88cb4e1
--- /dev/null
+++ b/haplohseq/patches/patch-src_HaplohSeq.cpp
@@ -0,0 +1,60 @@
+$NetBSD$
+
+--- src/HaplohSeq.cpp.orig	2025-01-26 13:47:41.918585702 +0000
++++ src/HaplohSeq.cpp
+@@ -195,14 +195,14 @@ void HaplohSeq::runBafHaplohseq(	std::st
+ 	for (unsigned int i = 0; i < numParamEventStarts; i++) {
+ 
+ 		// Create thread pool
+-		boost::asio::io_service ioService;
+-	//	boost::asio::io_service::work work(ioService);
+-		boost::shared_ptr<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
++		boost::asio::io_context ioService;
++	//	boost::asio::io_context::work work(ioService);
++		boost::shared_ptr<boost::asio::io_context::work> work(new boost::asio::io_context::work(ioService));
+ 		boost::thread_group threadPool;
+ 
+ 		// Spawn worker threads
+ 		for (std::size_t t = 0; t < numThreads; t++) {
+-			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_context::*)())&boost::asio::io_context::run, &ioService));
+ 		}
+ 
+ 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
+@@ -220,7 +220,7 @@ void HaplohSeq::runBafHaplohseq(	std::st
+ 
+ 			std::cout << "Posting job to thread pool for chromosome " << chr << "\n";
+ 			// IMPORTANT: do not pass shared_ptr by reference because the shared_ptr expects a new pointer to the object
+-			ioService.post(boost::bind(&HaplohSeq::runBafHaplohseqChr, this,
++			ioService.get_executor().post(boost::bind(&HaplohSeq::runBafHaplohseqChr, this,
+ 													chr,
+ 													boost::ref(chrHmms),
+ 													boost::ref(fp),
+@@ -413,14 +413,14 @@ void HaplohSeq::runVcfHaplohseq(	std::st
+ 	for (unsigned int i = 0; i < numParamEventStarts; i++) {
+ 
+ 		// Create thread pool
+-		boost::asio::io_service ioService;
+-	//	boost::asio::io_service::work work(ioService);
+-		boost::shared_ptr<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
++		boost::asio::io_context ioService;
++	//	boost::asio::io_context::work work(ioService);
++		boost::shared_ptr<boost::asio::io_context::work> work(new boost::asio::io_context::work(ioService));
+ 		boost::thread_group threadPool;
+ 
+ 		// Spawn worker threads
+ 		for (std::size_t t = 0; t < numThreads; t++) {
+-			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_context::*)())&boost::asio::io_context::run, &ioService));
+ 		}
+ 
+ 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
+@@ -438,7 +438,7 @@ void HaplohSeq::runVcfHaplohseq(	std::st
+ 
+ //			std::cout << "Posting job to thread pool for chromosome " << chr << "\n";
+ 			// IMPORTANT: do not pass shared_ptr by reference because the shared_ptr expects a new pointer to the object
+-			ioService.post(boost::bind(&HaplohSeq::runVcfHaplohseqChr, this,
++			ioService.get_executor().post(boost::bind(&HaplohSeq::runVcfHaplohseqChr, this,
+ 													chr,
+ 													boost::ref(chrHmms),
+ 													boost::ref(fp),


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