Attachment #194628 for bug #229330

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# $FreeBSD$

PORTNAME=	hisat2
PORTVERSION=	2.1.0
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/
DISTFILES=	${DISTNAME}-source${EXTRACT_SUFX}

MAINTAINER=	mzaki@niid.go.jp
COMMENT=	Graph-based alignment of sequencing reads to genomes

LICENSE=	GPLv3 ZLIB
LICENSE_COMB=	multi

ONLY_FOR_ARCHS=	amd64 i386
ONLY_FOR_ARCHS_REASON=	requires SSE2 instructions
.if empty(MACHINE_CPU:Msse2)
IGNORE=	this port requires SSE2
.endif

SCRIPTS=	${PORTNAME} ${PORTNAME}-build ${PORTNAME}-inspect ${PORTNAME}_*.py
DOCFILES=	MANUAL

USES=		gmake perl5 python:run shebangfix zip
USE_PERL5=	run
SHEBANG_FILES=	${SCRIPTS}

OPTIONS_DEFINE=	DOCS OPTIMIZED_CFLAGS POPCNT SRA
OPTIONS_DEFAULT_amd64=	${OPTIONS_DEFINE}
OPTIONS_DEFAULT_i386=	${OPTIONS_DEFINE:NPOPCNT}

OPTIMIZED_CFLAGS_CFLAGS=	-O3 -msse2 -funroll-loops

POPCNT_DESC=	POPCNT instruction support
POPCNT_MAKE_ARGS=	EXTRA_FLAGS=-DPOPCNT_CAPABILITY

SRA_DESC=	SRA data access support
SRA_BUILD_DEPENDS=	${LOCALBASE}/lib/libngs-c++-static.a:biology/ngs-sdk \
			${LOCALBASE}/lib/libncbi-vdb-static.a:biology/ncbi-vdb
SRA_LIB_DEPENDS=	libmbedtls.so:security/mbedtls
SRA_MAKE_ARGS=	USE_SRA=1 NCBI_NGS_DIR=${LOCALBASE} NCBI_VDB_DIR=${LOCALBASE}

do-install:
	${INSTALL_SCRIPT} ${SCRIPTS:S,^,${WRKSRC}/,} ${STAGEDIR}${PREFIX}/bin
	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-*-* ${STAGEDIR}${PREFIX}/bin

post-install-DOCS-on:
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}

.include <bsd.port.mk>

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(-)distinfo (+3 lines)
	1	TIMESTAMP = 1529634135
	2	SHA256 (hisat2-2.1.0-source.zip) = 89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781
	3	SIZE (hisat2-2.1.0-source.zip) = 3952939




--- Makefile.orig	2017-06-07 19:17:32 UTC
+++ Makefile
@@ -23,9 +23,9 @@
 INC =
 GCC_PREFIX = $(shell dirname `which gcc`)
 GCC_SUFFIX =
-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-CXX = $(CPP)
+CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+CXX ?= $(CPP)
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 0
@@ -55,7 +55,7 @@ ifneq (,$(findstring Darwin,$(shell unam
 	MACOS = 1
 endif
 
-EXTRA_FLAGS += -DPOPCNT_CAPABILITY
+#EXTRA_FLAGS += -DPOPCNT_CAPABILITY
 INC += -I third_party
 
 MM_DEF = 
@@ -94,9 +94,9 @@ SRA_LIB =
 SERACH_INC = 
 ifeq (1,$(USE_SRA))
 	SRA_DEF = -DUSE_SRA
-	SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
+	SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -lmbedtls -lmbedcrypto -lmbedx509 -lz -lbz2
 	SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
-	SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
+	SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib -L$(NCBI_VDB_DIR)/lib
 endif
 
 LIBS = $(PTHREAD_LIB)
@@ -135,7 +135,7 @@ VERSION = $(shell cat VERSION)
 
 # Convert BITS=?? to a -m flag
 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.
@@ -157,7 +157,7 @@ SSE_FLAG=-msse2
 
 DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
+RELEASE_FLAGS  = $(CFLAGS)
 RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
@@ -239,7 +239,7 @@ DEFS=-fno-strict-aliasing \
      -DHISAT2_VERSION="\"`cat VERSION`\"" \
      -DBUILD_HOST="\"`hostname`\"" \
      -DBUILD_TIME="\"`date`\"" \
-     -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
+     -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | grep version | tail -1`\"" \
      $(FILE_FLAGS) \
      $(PREF_DEF) \
      $(MM_DEF) \




https://github.com/infphilo/hisat2/commit/ddbd2552020d5eb4888e68eb8fa67b335f75fd31

--- aligner_result.cpp.orig	2016-09-28 12:05:47 UTC
+++ aligner_result.cpp
@@ -1264,7 +1264,7 @@ bool AlnFlags::printYF(BTString& o, bool
 	else if(!nfilt_  ) flag = "NS";
 	else if(!scfilt_ ) flag = "SC";
 	else if(!qcfilt_ ) flag = "QC";
-	if(flag > 0) {
+	if(*flag > 0) {
 		if(!first) o.append('\t');
 		o.append("YF:Z:");
 		o.append(flag);

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(-)files/patch-hisat2 (+11 lines)
	1	--- hisat2.orig 2018-06-22 03:58:33 UTC
	2	+++ hisat2
	3	@@ -45,7 +45,7 @@ while (-f $prog && -l $prog){
	4
	5	($vol,$script_path,$prog)
	6	= File::Spec->splitpath($prog);
	7	-my $os_is_nix = ($^O eq "linux") \|\| ($^O eq "darwin");
	8	+my $os_is_nix = 1;
	9	my $align_bin_s = $os_is_nix ? 'hisat2-align-s' : 'hisat2-align-s.exe';
	10	my $build_bin = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe';
	11	my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe';

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(-)pkg-descr (+11 lines)
	1	HISAT2 is a fast and sensitive alignment program for mapping next-generation
	2	sequencing reads to a population of genomes as well as to a single reference.
	3	HISAT2 is a successor to HISAT and TopHat2, both of which are spliced alignment
	4	program for mapping RNA-seq reads; additionally, HISAT2 is designed to map
	5	sequencing reads from genomic DNA of generic human population having SNPs.
	6
	7	Citation:
	8	Kim et al. (2015) HISAT: a fast spliced aligner with low memory requirements.
	9	Nature Methods 12: 357-360.
	10
	11	WWW: https://ccb.jhu.edu/software/hisat2/




bin/hisat2
bin/hisat2-align-l
bin/hisat2-align-s
bin/hisat2-build
bin/hisat2-build-l
bin/hisat2-build-s
bin/hisat2-inspect
bin/hisat2-inspect-l
bin/hisat2-inspect-s
bin/hisat2_extract_exons.py
bin/hisat2_extract_snps_haplotypes_UCSC.py
bin/hisat2_extract_snps_haplotypes_VCF.py
bin/hisat2_extract_splice_sites.py
bin/hisat2_simulate_reads.py
%%PORTDOCS%%%%DOCSDIR%%/MANUAL

Return to bug 229330

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(-)Makefile (+51 lines)
	1	# $FreeBSD$
	2
	3	PORTNAME= hisat2
	4	PORTVERSION= 2.1.0
	5	CATEGORIES= biology
	6	MASTER_SITES= ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/
	7	DISTFILES= ${DISTNAME}-source${EXTRACT_SUFX}
	8
	9	MAINTAINER= mzaki@niid.go.jp
	10	COMMENT= Graph-based alignment of sequencing reads to genomes
	11
	12	LICENSE= GPLv3 ZLIB
	13	LICENSE_COMB= multi
	14
	15	ONLY_FOR_ARCHS= amd64 i386
	16	ONLY_FOR_ARCHS_REASON= requires SSE2 instructions
	17	.if empty(MACHINE_CPU:Msse2)
	18	IGNORE= this port requires SSE2
	19	.endif
	20
	21	SCRIPTS= ${PORTNAME} ${PORTNAME}-build ${PORTNAME}-inspect ${PORTNAME}_*.py
	22	DOCFILES= MANUAL
	23
	24	USES= gmake perl5 python:run shebangfix zip
	25	USE_PERL5= run
	26	SHEBANG_FILES= ${SCRIPTS}
	27
	28	OPTIONS_DEFINE= DOCS OPTIMIZED_CFLAGS POPCNT SRA
	29	OPTIONS_DEFAULT_amd64= ${OPTIONS_DEFINE}
	30	OPTIONS_DEFAULT_i386= ${OPTIONS_DEFINE:NPOPCNT}
	31
	32	OPTIMIZED_CFLAGS_CFLAGS= -O3 -msse2 -funroll-loops
	33
	34	POPCNT_DESC= POPCNT instruction support
	35	POPCNT_MAKE_ARGS= EXTRA_FLAGS=-DPOPCNT_CAPABILITY
	36
	37	SRA_DESC= SRA data access support
	38	SRA_BUILD_DEPENDS= ${LOCALBASE}/lib/libngs-c++-static.a:biology/ngs-sdk \
	39	${LOCALBASE}/lib/libncbi-vdb-static.a:biology/ncbi-vdb
	40	SRA_LIB_DEPENDS= libmbedtls.so:security/mbedtls
	41	SRA_MAKE_ARGS= USE_SRA=1 NCBI_NGS_DIR=${LOCALBASE} NCBI_VDB_DIR=${LOCALBASE}
	42
	43	do-install:
	44	${INSTALL_SCRIPT} ${SCRIPTS:S,^,${WRKSRC}/,} ${STAGEDIR}${PREFIX}/bin
	45	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-- ${STAGEDIR}${PREFIX}/bin
	46
	47	post-install-DOCS-on:
	48	@${MKDIR} ${STAGEDIR}${DOCSDIR}
	49	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
	50
	51	.include <bsd.port.mk>

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(-)files/patch-Makefile (+63 lines)
	1	--- Makefile.orig 2017-06-07 19:17:32 UTC
	2	+++ Makefile
	3	@@ -23,9 +23,9 @@
	4	INC =
	5	GCC_PREFIX = $(shell dirname `which gcc`)
	6	GCC_SUFFIX =
	7	-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
	8	-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
	9	-CXX = $(CPP)
	10	+CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
	11	+CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
	12	+CXX ?= $(CPP)
	13	HEADERS = $(wildcard *.h)
	14	BOWTIE_MM = 1
	15	BOWTIE_SHARED_MEM = 0
	16	@@ -55,7 +55,7 @@ ifneq (,$(findstring Darwin,$(shell unam
	17	MACOS = 1
	18	endif
	19
	20	-EXTRA_FLAGS += -DPOPCNT_CAPABILITY
	21	+#EXTRA_FLAGS += -DPOPCNT_CAPABILITY
	22	INC += -I third_party
	23
	24	MM_DEF =
	25	@@ -94,9 +94,9 @@ SRA_LIB =
	26	SERACH_INC =
	27	ifeq (1,$(USE_SRA))
	28	SRA_DEF = -DUSE_SRA
	29	- SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
	30	+ SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -lmbedtls -lmbedcrypto -lmbedx509 -lz -lbz2
	31	SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
	32	- SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
	33	+ SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib -L$(NCBI_VDB_DIR)/lib
	34	endif
	35
	36	LIBS = $(PTHREAD_LIB)
	37	@@ -135,7 +135,7 @@ VERSION = $(shell cat VERSION)
	38
	39	# Convert BITS=?? to a -m flag
	40	BITS=32
	41	-ifeq (x86_64,$(shell uname -m))
	42	+ifeq (amd64,$(shell uname -m))
	43	BITS=64
	44	endif
	45	# msys will always be 32 bit so look at the cpu arch instead.
	46	@@ -157,7 +157,7 @@ SSE_FLAG=-msse2
	47
	48	DEBUG_FLAGS = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
	49	DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
	50	-RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
	51	+RELEASE_FLAGS = $(CFLAGS)
	52	RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
	53	NOASSERT_FLAGS = -DNDEBUG
	54	FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
	55	@@ -239,7 +239,7 @@ DEFS=-fno-strict-aliasing \
	56	-DHISAT2_VERSION="\"`cat VERSION`\"" \
	57	-DBUILD_HOST="\"`hostname`\"" \
	58	-DBUILD_TIME="\"`date`\"" \
	59	- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 \| tail -1`\"" \
	60	+ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 \| grep version \| tail -1`\"" \
	61	$(FILE_FLAGS) \
	62	$(PREF_DEF) \
	63	$(MM_DEF) \

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(-)files/patch-aligner__result.cpp (+13 lines)
	1	https://github.com/infphilo/hisat2/commit/ddbd2552020d5eb4888e68eb8fa67b335f75fd31
	2
	3	--- aligner_result.cpp.orig 2016-09-28 12:05:47 UTC
	4	+++ aligner_result.cpp
	5	@@ -1264,7 +1264,7 @@ bool AlnFlags::printYF(BTString& o, bool
	6	else if(!nfilt_ ) flag = "NS";
	7	else if(!scfilt_ ) flag = "SC";
	8	else if(!qcfilt_ ) flag = "QC";
	9	- if(flag > 0) {
	10	+ if(*flag > 0) {
	11	if(!first) o.append('\t');
	12	o.append("YF:Z:");
	13	o.append(flag);

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(-)pkg-plist (+15 lines)
	1	bin/hisat2
	2	bin/hisat2-align-l
	3	bin/hisat2-align-s
	4	bin/hisat2-build
	5	bin/hisat2-build-l
	6	bin/hisat2-build-s
	7	bin/hisat2-inspect
	8	bin/hisat2-inspect-l
	9	bin/hisat2-inspect-s
	10	bin/hisat2_extract_exons.py
	11	bin/hisat2_extract_snps_haplotypes_UCSC.py
	12	bin/hisat2_extract_snps_haplotypes_VCF.py
	13	bin/hisat2_extract_splice_sites.py
	14	bin/hisat2_simulate_reads.py
	15	%%PORTDOCS%%%%DOCSDIR%%/MANUAL