13 files changed, 308 insertions, 0 deletions

diff --git a/biology/haplohseq/Makefile b/biology/haplohseq/Makefile
new file mode 100644
index 000000000000..70d66fbe4e18
--- /dev/null
+++ b/biology/haplohseq/Makefile
@@ -0,0 +1,36 @@
+# $FreeBSD$
+
+PORTNAME=	haplohseq
+DISTVERSION=	0.1.2
+PORTREVISION=	2
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Identify regions of allelic imbalance
+
+LICENSE=	MIT
+
+LIB_DEPENDS=	libboost_system.so:devel/boost-libs
+RUN_DEPENDS=	R-cran-optparse>0:devel/R-cran-optparse
+
+USES=		compiler:c++11-lang gmake localbase:ldflags python
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	outpaddling
+
+OPTIONS_DEFINE=	EXAMPLES
+
+MAKEFILE=	makefile
+LDFLAGS+=	-lpthread
+MAKE_ENV=	STRIP=${STRIP}
+
+SUB_FILES=	haplohseq-example
+
+post-install-EXAMPLES-on:
+	${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${STAGEDIR}${PREFIX}/bin
+	(cd ${WRKSRC} && ${COPYTREE_SHARE} "example ldmap scripts" ${STAGEDIR}${EXAMPLESDIR})
+
+do-test:
+	@(cd ${WRKSRC}/build/test && ${FILESDIR}/run-tests)
+
+.include <bsd.port.mk>
diff --git a/biology/haplohseq/distinfo b/biology/haplohseq/distinfo
new file mode 100644
index 000000000000..a10bda0e1269
--- /dev/null
+++ b/biology/haplohseq/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1589733633
+SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0
+SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603
diff --git a/biology/haplohseq/files/haplohseq-example.in b/biology/haplohseq/files/haplohseq-example.in
new file mode 100644
index 000000000000..0cb2a5bee1d7
--- /dev/null
+++ b/biology/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 "$dir/example"
+sh ./example_run.sh
diff --git a/biology/haplohseq/files/patch-example_example__run.sh b/biology/haplohseq/files/patch-example_example__run.sh
new file mode 100644
index 000000000000..10a422bddd82
--- /dev/null
+++ b/biology/haplohseq/files/patch-example_example__run.sh
@@ -0,0 +1,24 @@
+--- example/example_run.sh.orig	2019-11-13 15:45:57 UTC
++++ example/example_run.sh
+@@ -1,4 +1,4 @@
+-#! /bin/bash
++#!/bin/sh
+ 
+ # Example:
+ # Identify allelic imbalance (AI) given a tumor 
+@@ -6,13 +6,13 @@
+ # of the GATK.  This involves the following 3 steps.
+ 
+ printf "STEP 1: PHASING 1KG HET SITES ...\n"
+-python ../scripts/simple_phaser.py \
++python2.7 ../scripts/simple_phaser.py \
+   --ldmap ../ldmap/hg19.exome.ldmap \
+   --vcf example_input/tumor_exome.vcf \
+   -o example_output/tumor_exome
+ 
+ printf "\nSTEP 2: IDENTIFYING REGIONS OF AI ...\n"
+-../haplohseq \
++haplohseq \
+   --vcf example_output/tumor_exome.hap.vcf \
+   --phased example_output/tumor_exome.hap \
+   --event_prevalence 0.1 \
diff --git a/biology/haplohseq/files/patch-makefile b/biology/haplohseq/files/patch-makefile
new file mode 100644
index 000000000000..5387716aa503
--- /dev/null
+++ b/biology/haplohseq/files/patch-makefile
@@ -0,0 +1,105 @@
+--- makefile.orig	2019-08-29 18:03:23 UTC
++++ makefile
+@@ -7,23 +7,32 @@
+ #
+ 
+ # Constants
+-CXX=g++
++# Default to g++ if not set by make args or environment
++CXX?=g++
+ #-O0 -g will turn on debugging
+ #The rule of thumb:
+ #When you need to debug, use -O0 (and -g to generate debugging symbols.)
+ #When you are preparing to ship it, use -O2.
+ #When you use gentoo, use -O3...!
+ #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.)
+-CXX_FLAGS=-Wall -g -stdlib=libstdc++
++# Use canonincal compiler variables, which may be provided by build env
++CXXFLAGS?=-Wall -g -stdlib=libstdc++
+ SRC=src
+ CONF=conf
+ HMM_SRC=$(SRC)/hmm
+ UTIL_SRC=$(SRC)/util
+-BOOST=/usr/local/boost_1_52_0
++BOOST?=/usr/local/boost_1_52_0
+ INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST)
+-LIBRARY_PATHS=-Llib/macosx 
++LIBRARY_PATHS?=-Llib/macosx
+ LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread
+ 
++# Installation target with destdir support
++DESTDIR?=.
++PREFIX?=/usr/local
++MKDIR?=mkdir
++INSTALL?=install
++STRIP?= # empty, set to -s to install stripped binary
++
+ # Generated directories which are generated in this script and cleaned up with 'make clean'
+ BUILD=build
+ OBJ=$(BUILD)/obj
+@@ -35,18 +44,21 @@ directories:
+ 
+ # Create object files into the OBJ directory from cpp files in the SRC directory.
+ $(OBJ)/%.o:	$(SRC)/%.cpp directories
+-	$(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++	$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+ $(OBJ)/%.o:	$(HMM_SRC)/%.cpp directories
+-	$(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++	$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+ $(OBJ)/%.o:	$(UTIL_SRC)/%.cpp directories
+-	$(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++	$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+ 
+-all: clean haplohseq
++all: haplohseq test
+ 
+ haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o
+-	$(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) 
+-	cp -r $(CONF) $(BIN)/.
+-	
++	$(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
++
++install:
++	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++	$(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin
++
+ clean:
+ 	rm -rf $(BUILD)
+ 
+@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess
+ 
+ # Create test object files into the OBJ directory from cpp files in the SRC directory.
+ $(TEST_BIN)/%.o:	$(TEST_SRC)/%.cpp directories test_directory
+-	$(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
++	$(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
+ 
+ HaplohSeqTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 
+ FreqPhaseTest:	$(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 
+ HmmTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 
+ InputProcessorTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 	
+ MathUtilTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 	
+ ReporterTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) 
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ 
+ ThreadPoolTest:	$(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o
+-	$(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++	$(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ ############################## END TEST LOGIC ##############################
+ 
+ 
diff --git a/biology/haplohseq/files/patch-scripts_ldmap.py b/biology/haplohseq/files/patch-scripts_ldmap.py
new file mode 100644
index 000000000000..d16f74cf9949
--- /dev/null
+++ b/biology/haplohseq/files/patch-scripts_ldmap.py
@@ -0,0 +1,8 @@
+--- scripts/ldmap.py.orig	2019-11-13 15:51:02 UTC
++++ scripts/ldmap.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/env python2.7
++
+ import argparse
+ import sys
+ import random
diff --git a/biology/haplohseq/files/patch-scripts_simple__phaser.py b/biology/haplohseq/files/patch-scripts_simple__phaser.py
new file mode 100644
index 000000000000..d81d288e67ea
--- /dev/null
+++ b/biology/haplohseq/files/patch-scripts_simple__phaser.py
@@ -0,0 +1,8 @@
+--- scripts/simple_phaser.py.orig	2019-11-13 15:52:02 UTC
++++ scripts/simple_phaser.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/env python2.7
++
+ import argparse
+ import random
+ import sys
diff --git a/biology/haplohseq/files/patch-src_FreqPhase.cpp b/biology/haplohseq/files/patch-src_FreqPhase.cpp
new file mode 100644
index 000000000000..9bab76aee2f5
--- /dev/null
+++ b/biology/haplohseq/files/patch-src_FreqPhase.cpp
@@ -0,0 +1,29 @@
+--- src/FreqPhase.cpp.orig	2019-11-13 14:19:06 UTC
++++ src/FreqPhase.cpp
+@@ -5,6 +5,7 @@
+  * Email:  sanlucas@gmail.com
+  */
+ 
++#include <sysexits.h>
+ #include "FreqPhase.h"
+ 
+ namespace haplohseq {
+@@ -180,10 +181,17 @@ double FreqPhase::meanValue(const std::v
+ double FreqPhase::medianValue(const std::vector<double>& values) {
+ 	double median;
+ 	size_t size = values.size();
++
++	// We can probably detect this condition earlier while loading the VCF
++	if ( size == 0 ) {
++		std::cerr << "FreqPhase::medianValue(): values vector is empty." << std::endl;
++		std::cerr << "Make sure your VCF has all of GT:AD:DP in the FORMAT column." << std::endl;
++		exit(EX_DATAERR);
++	}
+ 	std::vector<double> tempFreqs(values);
+ 	sort(tempFreqs.begin(), tempFreqs.end());
+ 
+-	if (size  % 2 == 0) {
++	if (size % 2 == 0) {
+ 		median = (tempFreqs[size / 2 - 1] + tempFreqs[size / 2]) / 2;
+ 	}
+ 	else {
diff --git a/biology/haplohseq/files/patch-src_HaplohSeq.cpp b/biology/haplohseq/files/patch-src_HaplohSeq.cpp
new file mode 100644
index 000000000000..a80ce577f747
--- /dev/null
+++ b/biology/haplohseq/files/patch-src_HaplohSeq.cpp
@@ -0,0 +1,20 @@
+--- src/HaplohSeq.cpp.orig	2019-09-01 14:58:30 UTC
++++ src/HaplohSeq.cpp
+@@ -202,7 +202,7 @@ void HaplohSeq::runBafHaplohseq(	std::string& obsType,
+ 
+ 		// Spawn worker threads
+ 		for (std::size_t t = 0; t < numThreads; t++) {
+-			threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
+ 		}
+ 
+ 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
+@@ -420,7 +420,7 @@ void HaplohSeq::runVcfHaplohseq(	std::string& obsType,
+ 
+ 		// Spawn worker threads
+ 		for (std::size_t t = 0; t < numThreads; t++) {
+-			threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
+ 		}
+ 
+ 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
diff --git a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp
new file mode 100644
index 000000000000..21ea56a8f600
--- /dev/null
+++ b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp
@@ -0,0 +1,11 @@
+--- src/test/InputProcessorTest.cpp.orig	2019-09-01 12:33:22 UTC
++++ src/test/InputProcessorTest.cpp
+@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(isHetTest) {
+ 	BOOST_REQUIRE_EQUAL(inputProc.isHet('A','?'), false);
+ 	BOOST_REQUIRE_EQUAL(inputProc.isHet('A','.'), false);
+ 	BOOST_REQUIRE_EQUAL(inputProc.isHet('A',' '), false);
+-	BOOST_REQUIRE_EQUAL(inputProc.isHet('C', NULL), true);
++	BOOST_REQUIRE_EQUAL(inputProc.isHet('C','\0'), true);
+ }
+ 
+ BOOST_AUTO_TEST_CASE(readAllelesTest) {
diff --git a/biology/haplohseq/files/run-tests b/biology/haplohseq/files/run-tests
new file mode 100644
index 000000000000..1ecc6ebc5e35
--- /dev/null
+++ b/biology/haplohseq/files/run-tests
@@ -0,0 +1,10 @@
+#!/bin/sh -e
+
+printf "\n=== FreqPhaseTest ===\n\n"
+./FreqPhaseTest
+printf "\n=== InputProcessorTest ===\n\n"
+./InputProcessorTest
+printf "\n=== HmmTest ===\n\n"
+./HmmTest
+printf "\n=== HaplohSeqTest ===\n\n"
+./HaplohSeqTest
diff --git a/biology/haplohseq/pkg-descr b/biology/haplohseq/pkg-descr
new file mode 100644
index 000000000000..751d6d58268d
--- /dev/null
+++ b/biology/haplohseq/pkg-descr
@@ -0,0 +1,6 @@
+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.
+
+WWW: https://sites.google.com/site/integrativecancergenomics/software/haplohseq
diff --git a/biology/haplohseq/pkg-plist b/biology/haplohseq/pkg-plist
new file mode 100644
index 000000000000..cab57d2be449
--- /dev/null
+++ b/biology/haplohseq/pkg-plist
@@ -0,0 +1,11 @@
+bin/haplohseq
+%%PORTEXAMPLES%%bin/haplohseq-example
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/example/example_input/tumor_exome.vcf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/example/example_run.sh
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ldmap/hg19.exome.ldmap
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/haplohseq_plot.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py.orig
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py.orig
+%%PORTEXAMPLES%%@dir %%EXAMPLESDIR%%/example/example_output