Attachment #192188 for bug #227272




# Created by: Scott Cheloha <scottcheloha@gmail.com>
# $FreeBSD: head/biology/bedtools/Makefile 456976 2017-12-22 12:27:14Z amdmi3 $

PORTNAME=	bedtools
PORTVERSION=	2.25.0
DISTVERSIONPREFIX=	v
DISTVERSION=	2.27.1
CATEGORIES=	biology
MASTER_SITES=	GITHUB

MAINTAINER=	scottcheloha@gmail.com
COMMENT=	Toolset for genome set arithmetic such as intersect, union

LICENSE=	GPLv2
LICENSE_FILE=	${WRKSRC}/LICENSE

USES=		gmake python
USE_GITHUB=	yes
GH_ACCOUNT=	arq5x
GH_PROJECT=	bedtools2

USES=		gmake python
#NO_ARCH=	yes

MAKE_JOBS_UNSAFE=	yes

post-patch:
	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile

post-install:
	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)/usr/ports/wip/bedtools/distinfo (-2 / +3 lines)
1	SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb	1	TIMESTAMP = 1519746174
2	SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049	2	SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
		3	SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119




--- Makefile.orig	2017-12-14 17:15:02 UTC
+++ Makefile
@@ -4,7 +4,7 @@
 # (c) 2009 Aaron Quinlan

 export SRC_DIR	= src
 export UTIL_DIR	= src/utils
-export CXX		= g++
+export CXX		?= g++
 ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 else
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 endif
 export LIBS		= -lz
 export BT_ROOT  = src/utils/BamTools/
@@ -129,20 +129,17 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
 				-I$(SRC_DIR)/utils/GenomeFile \
 				-I$(SRC_DIR)/utils/RecordOutputMgr \
 				-I$(SRC_DIR)/utils/ToolBase \
-				-I$(SRC_DIR)/utils/driver \
-				
+				-I$(SRC_DIR)/utils/driver
 
 all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
 	@echo "- Building main bedtools binary."
 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
 	@echo "done."
-	
 	@echo "- Creating executables for old CLI."
 	@python scripts/makeBashScripts.py
 	@chmod +x bin/*
 	@echo "done."
-	
 
 # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
@@ -193,7 +193,7 @@ clean:
@@ -183,7 +180,7 @@ clean:
 .PHONY: clean
 
 test: all

Lines 1-11 Link Here

(-)/usr/ports/wip/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h (-11 lines)
1	--- src/utils/FileRecordTools/Records/StrandQueue.h.orig 2015-09-03 04:36:18 UTC
2	+++ src/utils/FileRecordTools/Records/StrandQueue.h
3	@@ -30,7 +30,7 @@ public:
4
5	private:
6	// static RecordPtrSortFunctor _recSortFunctor;
7	- typedef priority_queue<Record , vector<const Record >, RecordPtrSortDescFunctor > queueType;
8	+ typedef priority_queue<Record , vector<Record >, RecordPtrSortDescFunctor > queueType;
9	vector<queueType *> _queues;
10	static const int NUM_QUEUES = 3;
11

Lines 1-7 Link Here

(-)/usr/ports/wip/bedtools/pkg-descr (-2 / +2 lines)
1	The bedtools utilities are a suite of tools for performing a wide range of	1	The bedtools utilities are a suite of tools for performing a wide range of
2	genomics analysis tasks. The most widely-used of these tools enable genome	2	genomics analysis tasks. The most widely-used of these tools enable genome
3	arithmetic, i.e., set theory on the genome. For example, with bedtools one	3	arithmetic, i.e., set theory on the genome. For example, with bedtools one can
4	can intersect, merge, count, complement, and shuffle genomic intervals from	4	intersect, merge, count, complement, and shuffle genomic intervals from
5	multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.	5	multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
6		6
7	Although each individual utility is designed to do a relatively simple task,	7	Although each individual utility is designed to do a relatively simple task,

Lines 27-32 Link Here

(-)/usr/ports/wip/bedtools/pkg-plist (+1 lines)
27	bin/pairToBed	27	bin/pairToBed
28	bin/pairToPair	28	bin/pairToPair
29	bin/randomBed	29	bin/randomBed
		30	bin/shiftBed
30	bin/shuffleBed	31	bin/shuffleBed
31	bin/slopBed	32	bin/slopBed
32	bin/sortBed	33	bin/sortBed

Return to bug 227272

Lines 1-29 Link Here

(-)/usr/ports/wip/bedtools/Makefile (-11 / +7 lines)
1	# Created by: Scott Cheloha <scottcheloha@gmail.com>
2	# $FreeBSD: head/biology/bedtools/Makefile 456976 2017-12-22 12:27:14Z amdmi3 $	1	# $FreeBSD: head/biology/bedtools/Makefile 456976 2017-12-22 12:27:14Z amdmi3 $
3		2
4	PORTNAME= bedtools	3	PORTNAME= bedtools
5	PORTVERSION= 2.25.0
6	DISTVERSIONPREFIX= v	4	DISTVERSIONPREFIX= v
		5	DISTVERSION= 2.27.1
7	CATEGORIES= biology	6	CATEGORIES= biology
8	MASTER_SITES= GITHUB
9		7
10	MAINTAINER= scottcheloha@gmail.com	8	MAINTAINER= scottcheloha@gmail.com
11	COMMENT= Toolset for genome arithmetic	9	COMMENT= Toolset for genome set arithmetic such as intersect, union
12		10
13	LICENSE= GPLv2	11	LICENSE= GPLv2
14	LICENSE_FILE= ${WRKSRC}/LICENSE	12	LICENSE_FILE= ${WRKSRC}/LICENSE
15		13
		14	USES= gmake python
16	USE_GITHUB= yes	15	USE_GITHUB= yes
17	GH_ACCOUNT= arq5x	16	GH_ACCOUNT= arq5x
18	GH_PROJECT= bedtools2	17	GH_PROJECT= bedtools2
19		18
20	USES= gmake python
21	#NO_ARCH= yes
22
23	MAKE_JOBS_UNSAFE= yes
24
25	post-patch:	19	post-patch:
26	@${REINPLACE_CMD} -e 's\|python\|${PYTHON_CMD}\|g' \	20	@${REINPLACE_CMD} -e 's\|python\|${PYTHON_CMD}\|g' ${WRKSRC}/Makefile
27	${WRKSRC}/Makefile	21
		22	post-install:
		23	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
28		24
29	.include <bsd.port.mk>	25	.include <bsd.port.mk>

Lines 1-4 Link Here

(-)/usr/ports/wip/bedtools/files/patch-Makefile (-31 / +10 lines)
1	--- Makefile.orig 2015-11-14 00:48:48 UTC	1	--- Makefile.orig 2017-12-14 17:15:02 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -4,7 +4,7 @@	3	@@ -4,7 +4,7 @@
4	# (c) 2009 Aaron Quinlan	4	# (c) 2009 Aaron Quinlan
Lines 14-51 Link Here
14	export SRC_DIR = src	14	export SRC_DIR = src
15	export UTIL_DIR = src/utils	15	export UTIL_DIR = src/utils
16	-export CXX = g++	16	-export CXX = g++
17	+export CXX = c++	17	+export CXX ?= g++
18	#ifeq ($(DEBUG),1)	18	ifeq ($(DEBUG),1)
19	#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG	19	-export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
20	#else	20	+export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
		21	else
21	-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)	22	-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
22	+export CXXFLAGS += -Wall -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)	23	+export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
23	#endif	24	endif
24	export LIBS = -lz
25	export BT_ROOT = src/utils/BamTools/
26	@@ -129,20 +129,17 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
27	-I$(SRC_DIR)/utils/GenomeFile \
28	-I$(SRC_DIR)/utils/RecordOutputMgr \
29	-I$(SRC_DIR)/utils/ToolBase \
30	- -I$(SRC_DIR)/utils/driver \
31	-
32	+ -I$(SRC_DIR)/utils/driver
33
34	all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
35	@echo "- Building main bedtools binary."
36	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
37	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
38	@echo "done."
39	-
40	@echo "- Creating executables for old CLI."
41	@python scripts/makeBashScripts.py
42	@chmod +x bin/*
43	@echo "done."
44	-
45		25
46	.PHONY: all	26	# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
47		27	@@ -193,7 +193,7 @@ clean:
48	@@ -183,7 +180,7 @@ clean:
49	.PHONY: clean	28	.PHONY: clean
50		29
51	test: all	30	test: all