Attachment #230078 for bug #260389

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PORTNAME=		bowtie
DISTVERSIONPREFIX=	v
DISTVERSION=		1.3.1
PORTREVISION=		9
CATEGORIES=		biology

MAINTAINER=	jwb@FreeBSD.org

LICENSE=	ART10

# May also work on other 64-bit platforms, but untested
ONLY_FOR_ARCHS=	amd64 powerpc64 powerpc64le

# FIXME: bowtie-align intermittently dumps core when compiled with clang
# GCC 4.2 does not provide good performance
USES=		compiler:gcc-c++11-lib gmake perl5 python:run shebangfix
USE_GCC=	yes
USE_PERL5=	run
USE_GITHUB=	yes

SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build scripts/bowtie-hbb.sh \
		bowtie-inspect
GH_ACCOUNT=	BenLangmead

OPTIONS_DEFINE=	DOCS

.include <bsd.port.options.mk>

.if ${ARCH:Mpowerpc64*}
MAKE_ENV=	POPCNT_CAPABILITY=0
.endif

post-install:
	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
	${INSTALL_SCRIPT} \

Lines 1-2 Link Here

(-)biology/bowtie/distinfo (-2 / +3 lines)
1	SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7	1	TIMESTAMP = 1639406970
2	SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346	2	SHA256 (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573
		3	SIZE (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 7672741




--- Makefile.orig	2015-06-23 16:32:51 UTC
+++ Makefile
@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
 SEQAN_DIR = SeqAn-1.1
 SEQAN_INC = -I $(SEQAN_DIR)
 INC = $(SEQAN_INC) -I third_party
-CPP = g++
-CXX = $(CPP)
-CC = gcc
+
+# Use ?= to allow environment CPP, CC, CXX to take precedence.  This avoids
+# the need to modify the Makefile on different platforms.  Package managers
+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
+CPP ?= g++
+CXX ?= $(CPP)
+CC ?= gcc
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 1
@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
 PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
 
 ifeq (1,$(WITH_TBB))
-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
+	LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
 	EXTRA_FLAGS += -DWITH_TBB
 else
-	LIBS = $(PTHREAD_LIB)
+	LIBS = ${LDFLAGS} $(PTHREAD_LIB)
 endif
 
 SEARCH_LIBS = 
@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
 VERSION = $(shell cat VERSION)
 
 BITS=32
-ifeq (x86_64,$(shell uname -m))
+ifeq (amd64,$(shell uname -m))
 	BITS=64
 endif
 # msys will always be 32 bit so look at the cpu arch instead.
@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
     $(error bowtie2 compilation requires a 64-bit platform )
 endif
 
-DEBUG_FLAGS = -O0 -g3 -m64
-RELEASE_FLAGS = -O3 -m64
+DEBUG_FLAGS = -O0 -g3
+RELEASE_FLAGS = -O
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 

Lines 1-11 Link Here

(-)biology/bowtie/files/patch-ebwt.h (-11 lines)
1	--- ebwt.h.orig 2018-11-03 20:51:56 UTC
2	+++ ebwt.h
3	@@ -860,7 +860,7 @@ public:
4	TIndexOffU* ftab() const { return _ftab; }
5	TIndexOffU* eftab() const { return _eftab; }
6	TIndexOffU* offs() const { return _offs; }
7	- uint32_t* isa() const { return _isa; } /* check */
8	+ uint32_t* isa() const { return (uint32_t)_isa; } /* check */
9	TIndexOffU* plen() const { return _plen; }
10	TIndexOffU* rstarts() const { return _rstarts; }
11	uint8_t* ebwt() const { return _ebwt; }

Lines 1-11 Link Here

(-)biology/bowtie/files/patch-processor__support.h (-11 lines)
1	--- processor_support.h.orig 2020-07-04 10:42:26 UTC
2	+++ processor_support.h
3	@@ -49,7 +49,7 @@ class ProcessorSupport { (public)
4	#elif defined(USING_GCC_COMPILER)
5	__get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
6	#else
7	- std::cerr << “ERROR: please define __cpuid() for this build.\n”;
8	+ std::cerr << "ERROR: please define __cpuid() for this build.\n";
9	assert(0);
10	#endif
11	if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;




%%DATADIR%%/reads/e_coli_1000_1.fq
%%DATADIR%%/reads/e_coli_1000_2.fa
%%DATADIR%%/reads/e_coli_1000_2.fq
%%DATADIR%%/reads/e_coli_1000_interleaved.fq
%%DATADIR%%/scripts/best_verify.pl
%%DATADIR%%/scripts/bowtie-hbb.sh
%%DATADIR%%/scripts/bs_mapability.pl
%%DATADIR%%/scripts/build_test.sh
%%DATADIR%%/scripts/colorize_fasta.pl

%%DATADIR%%/scripts/pe_verify.pl
%%DATADIR%%/scripts/reconcile_alignments.pl
%%DATADIR%%/scripts/reconcile_alignments_pe.pl
%%DATADIR%%/scripts/run-hbb.sh
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/manual.html
%%PORTDOCS%%%%DOCSDIR%%/release.txt

%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi
%%PORTDOCS%%%%DOCSDIR%%/website/push.sh
%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi

Return to bug 260389

Lines 1-7 Link Here

(-)biology/bowtie/Makefile (-6 / +11 lines)
1	PORTNAME= bowtie	1	PORTNAME= bowtie
2	DISTVERSIONPREFIX= v	2	DISTVERSIONPREFIX= v
3	DISTVERSION= 1.1.2	3	DISTVERSION= 1.3.1
4	PORTREVISION= 9
5	CATEGORIES= biology	4	CATEGORIES= biology
6		5
7	MAINTAINER= jwb@FreeBSD.org	6	MAINTAINER= jwb@FreeBSD.org
Lines 10-29 COMMENT= Ultrafast, memory-efficient short read aligne Link Here
10	LICENSE= ART10	9	LICENSE= ART10
11		10
12	# May also work on other 64-bit platforms, but untested	11	# May also work on other 64-bit platforms, but untested
13	ONLY_FOR_ARCHS= amd64	12	ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le
14		13
15	# FIXME: bowtie-align intermittently dumps core when compiled with clang	14	# FIXME: bowtie-align intermittently dumps core when compiled with clang
16	# GCC 4.2 does not provide good performance	15	# GCC 4.2 does not provide good performance
17	USES= gmake perl5 python:run shebangfix	16	USES= compiler:gcc-c++11-lib gmake perl5 python:run shebangfix
18	USE_GCC= yes
19	USE_PERL5= run	17	USE_PERL5= run
20	USE_GITHUB= yes	18	USE_GITHUB= yes
21		19
22	SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect	20	SHEBANG_FILES= scripts/*.pl bowtie bowtie-build scripts/bowtie-hbb.sh \
		21	bowtie-inspect
23	GH_ACCOUNT= BenLangmead	22	GH_ACCOUNT= BenLangmead
24		23
25	OPTIONS_DEFINE= DOCS	24	OPTIONS_DEFINE= DOCS
26		25
		26	.include <bsd.port.options.mk>
		27
		28	.if ${ARCH:Mpowerpc64*}
		29	MAKE_ENV= POPCNT_CAPABILITY=0
		30	.endif
		31
27	post-install:	32	post-install:
28	${MKDIR} ${STAGEDIR}${DATADIR}/scripts	33	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
29	${INSTALL_SCRIPT} \	34	${INSTALL_SCRIPT} \

Lines 1-52 Link Here

(-)biology/bowtie/files/patch-Makefile (-52 lines)
1	--- Makefile.orig 2015-06-23 16:32:51 UTC
2	+++ Makefile
3	@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
4	SEQAN_DIR = SeqAn-1.1
5	SEQAN_INC = -I $(SEQAN_DIR)
6	INC = $(SEQAN_INC) -I third_party
7	-CPP = g++
8	-CXX = $(CPP)
9	-CC = gcc
10	+
11	+# Use ?= to allow environment CPP, CC, CXX to take precedence. This avoids
12	+# the need to modify the Makefile on different platforms. Package managers
13	+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
14	+CPP ?= g++
15	+CXX ?= $(CPP)
16	+CC ?= gcc
17	HEADERS = $(wildcard *.h)
18	BOWTIE_MM = 1
19	BOWTIE_SHARED_MEM = 1
20	@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
21	PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
22
23	ifeq (1,$(WITH_TBB))
24	- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
25	+ LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
26	EXTRA_FLAGS += -DWITH_TBB
27	else
28	- LIBS = $(PTHREAD_LIB)
29	+ LIBS = ${LDFLAGS} $(PTHREAD_LIB)
30	endif
31
32	SEARCH_LIBS =
33	@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
34	VERSION = $(shell cat VERSION)
35
36	BITS=32
37	-ifeq (x86_64,$(shell uname -m))
38	+ifeq (amd64,$(shell uname -m))
39	BITS=64
40	endif
41	# msys will always be 32 bit so look at the cpu arch instead.
42	@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
43	$(error bowtie2 compilation requires a 64-bit platform )
44	endif
45
46	-DEBUG_FLAGS = -O0 -g3 -m64
47	-RELEASE_FLAGS = -O3 -m64
48	+DEBUG_FLAGS = -O0 -g3
49	+RELEASE_FLAGS = -O
50	NOASSERT_FLAGS = -DNDEBUG
51	FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
52

Lines 26-32 bin/bowtie-inspect-s Link Here

(-)biology/bowtie/pkg-plist (-1 / +4 lines)
26	%%DATADIR%%/reads/e_coli_1000_1.fq	26	%%DATADIR%%/reads/e_coli_1000_1.fq
27	%%DATADIR%%/reads/e_coli_1000_2.fa	27	%%DATADIR%%/reads/e_coli_1000_2.fa
28	%%DATADIR%%/reads/e_coli_1000_2.fq	28	%%DATADIR%%/reads/e_coli_1000_2.fq
		29	%%DATADIR%%/reads/e_coli_1000_interleaved.fq
29	%%DATADIR%%/scripts/best_verify.pl	30	%%DATADIR%%/scripts/best_verify.pl
		31	%%DATADIR%%/scripts/bowtie-hbb.sh
30	%%DATADIR%%/scripts/bs_mapability.pl	32	%%DATADIR%%/scripts/bs_mapability.pl
31	%%DATADIR%%/scripts/build_test.sh	33	%%DATADIR%%/scripts/build_test.sh
32	%%DATADIR%%/scripts/colorize_fasta.pl	34	%%DATADIR%%/scripts/colorize_fasta.pl
Lines 58-63 bin/bowtie-inspect-s Link Here
58	%%DATADIR%%/scripts/pe_verify.pl	60	%%DATADIR%%/scripts/pe_verify.pl
59	%%DATADIR%%/scripts/reconcile_alignments.pl	61	%%DATADIR%%/scripts/reconcile_alignments.pl
60	%%DATADIR%%/scripts/reconcile_alignments_pe.pl	62	%%DATADIR%%/scripts/reconcile_alignments_pe.pl
		63	%%DATADIR%%/scripts/run-hbb.sh
61	%%PORTDOCS%%%%DOCSDIR%%/README	64	%%PORTDOCS%%%%DOCSDIR%%/README
62	%%PORTDOCS%%%%DOCSDIR%%/manual.html	65	%%PORTDOCS%%%%DOCSDIR%%/manual.html
63	%%PORTDOCS%%%%DOCSDIR%%/release.txt	66	%%PORTDOCS%%%%DOCSDIR%%/release.txt
Lines 81-87 bin/bowtie-inspect-s Link Here
81	%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi	84	%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
82	%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml	85	%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
83	%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi	86	%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi
84	%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh	87	%%PORTDOCS%%%%DOCSDIR%%/website/push.sh
85	%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi	88	%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
86	%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi	89	%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
87	%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi	90	%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi