Attachment #180156 for bug #216619

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Lines 2-8 Link Here

(-)/usr/wip/biology/bowtie2/Makefile (-1 / +3 lines)
2	# $FreeBSD: head/biology/bowtie2/Makefile 429003 2016-12-20 17:01:27Z jrm $	2	# $FreeBSD: head/biology/bowtie2/Makefile 429003 2016-12-20 17:01:27Z jrm $
3		3
4	PORTNAME= bowtie2	4	PORTNAME= bowtie2
5	PORTVERSION= 2.2.9	5	PORTVERSION= 2.3.0
6	DISTVERSIONPREFIX= v	6	DISTVERSIONPREFIX= v
7	CATEGORIES= biology	7	CATEGORIES= biology
8		8
Lines 12-17 Link Here
12	LICENSE= GPLv3+	12	LICENSE= GPLv3+
13	LICENSE_FILE= ${WRKSRC}/LICENSE	13	LICENSE_FILE= ${WRKSRC}/LICENSE
14		14
		15	LIB_DEPENDS+= libtbb.so:devel/tbb
		16
15	# May also work on other 64-bit platforms, but untested	17	# May also work on other 64-bit platforms, but untested
16	ONLY_FOR_ARCHS= amd64	18	ONLY_FOR_ARCHS= amd64
17	USES= gmake perl5 python shebangfix	19	USES= gmake perl5 python shebangfix

Lines 1-3 Link Here

(-)/usr/wip/biology/bowtie2/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1475861880	1	TIMESTAMP = 1487550143
2	SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee	2	SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
3	SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106	3	SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016




--- Makefile.orig	2016-12-30 09:40:06.000000000 -0600
+++ Makefile	2017-02-19 18:55:16.371000000 -0600
@@ -21,8 +21,8 @@
 # Makefile for bowtie, bowtie2-build, bowtie2-inspect
 #

 
 INC =
 GCC_PREFIX = $(shell dirname `which gcc`)
@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
     INC += -I third_party
 endif
 
+INC += -I ${LOCALBASE}/include
+
 MM_DEF =
 
 ifeq (1,$(BOWTIE_MM))
@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
 endif
 
 PTHREAD_PKG =
-PTHREAD_LIB =
+PTHREAD_LIB = 
 
 #if we're not using TBB, then we can't use queuing locks
 ifeq (1,$(NO_TBB))
@@ -94,7 +96,7 @@ endif
 
 #default is to use Intel TBB
 ifneq (1,$(NO_TBB))
-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
+	LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
 	override EXTRA_FLAGS += -DWITH_TBB
 else
 	LIBS = $(PTHREAD_LIB)
@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
 
 DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""

Line 0 Link Here

(-)/usr/wip/biology/bowtie2/files/patch-aligner__result.cpp (+11 lines)
	1	--- aligner_result.cpp.orig 2017-02-19 18:40:54.398991000 -0600
	2	+++ aligner_result.cpp 2017-02-19 18:41:14.093250000 -0600
	3	@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
	4	else if(!nfilt_ ) flag = "NS";
	5	else if(!scfilt_ ) flag = "SC";
	6	else if(!qcfilt_ ) flag = "QC";
	7	- if(flag > 0) {
	8	+ if(*flag != '\0') {
	9	if(!first) o.append('\t');
	10	o.append("YF:Z:");
	11	o.append(flag);

Return to bug 216619

Lines 1-5 Link Here

(-)/usr/wip/biology/bowtie2/files/patch-Makefile (-3 / +30 lines)
1	--- Makefile.orig 2016-02-11 17:20:57 UTC	1	--- Makefile.orig 2016-12-30 09:40:06.000000000 -0600
2	+++ Makefile	2	+++ Makefile 2017-02-19 18:55:16.371000000 -0600
3	@@ -21,8 +21,8 @@	3	@@ -21,8 +21,8 @@
4	# Makefile for bowtie, bowtie2-build, bowtie2-inspect	4	# Makefile for bowtie, bowtie2-build, bowtie2-inspect
5	#	5	#
Lines 11-17 Link Here
11		11
12	INC =	12	INC =
13	GCC_PREFIX = $(shell dirname `which gcc`)	13	GCC_PREFIX = $(shell dirname `which gcc`)
14	@@ -169,7 +169,7 @@ SSE_FLAG=-msse2	14	@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
		15	INC += -I third_party
		16	endif
		17
		18	+INC += -I ${LOCALBASE}/include
		19	+
		20	MM_DEF =
		21
		22	ifeq (1,$(BOWTIE_MM))
		23	@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
		24	endif
		25
		26	PTHREAD_PKG =
		27	-PTHREAD_LIB =
		28	+PTHREAD_LIB =
		29
		30	#if we're not using TBB, then we can't use queuing locks
		31	ifeq (1,$(NO_TBB))
		32	@@ -94,7 +96,7 @@ endif
		33
		34	#default is to use Intel TBB
		35	ifneq (1,$(NO_TBB))
		36	- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
		37	+ LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
		38	override EXTRA_FLAGS += -DWITH_TBB
		39	else
		40	LIBS = $(PTHREAD_LIB)
		41	@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
15		42
16	DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)	43	DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)
17	DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""	44	DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""