Attachment 194628 Details for Bug 229330 – svn diff

[patch] svn diff

hisat2-2.1.0.diff (text/plain), 9.14 KB, created by Motomichi Matsuzaki on 2018-06-25 09:15:50 UTC

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Creator: Motomichi Matsuzaki

Created: 2018-06-25 09:15:50 UTC

Size: 9.14 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(nonexistent)
>+++ Makefile	(working copy)
>@@ -0,0 +1,51 @@
>+# $FreeBSD$
>+
>+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>
>
>Property changes on: Makefile
>___________________________________________________________________
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:keywords
>## -0,0 +1 ##
>+FreeBSD=%H
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: distinfo
>===================================================================
>--- distinfo	(nonexistent)
>+++ distinfo	(working copy)
>@@ -0,0 +1,3 @@
>+TIMESTAMP = 1529634135
>+SHA256 (hisat2-2.1.0-source.zip) = 89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781
>+SIZE (hisat2-2.1.0-source.zip) = 3952939
>
>Property changes on: distinfo
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(nonexistent)
>+++ files/patch-Makefile	(working copy)
>@@ -0,0 +1,63 @@
>+--- 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) \
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-aligner__result.cpp
>===================================================================
>--- files/patch-aligner__result.cpp	(nonexistent)
>+++ files/patch-aligner__result.cpp	(working copy)
>@@ -0,0 +1,13 @@
>+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);
>
>Property changes on: files/patch-aligner__result.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-hisat2
>===================================================================
>--- files/patch-hisat2	(nonexistent)
>+++ files/patch-hisat2	(working copy)
>@@ -0,0 +1,11 @@
>+--- hisat2.orig	2018-06-22 03:58:33 UTC
>++++ hisat2
>+@@ -45,7 +45,7 @@ while (-f $prog && -l $prog){
>+ 
>+ ($vol,$script_path,$prog) 
>+                 = File::Spec->splitpath($prog);
>+-my $os_is_nix   = ($^O eq "linux") || ($^O eq "darwin");
>++my $os_is_nix   = 1;
>+ my $align_bin_s = $os_is_nix ? 'hisat2-align-s' : 'hisat2-align-s.exe'; 
>+ my $build_bin   = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe';               
>+ my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe'; 
>
>Property changes on: files/patch-hisat2
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(nonexistent)
>+++ pkg-descr	(working copy)
>@@ -0,0 +1,11 @@
>+HISAT2 is a fast and sensitive alignment program for mapping next-generation
>+sequencing reads to a population of genomes as well as to a single reference.
>+HISAT2 is a successor to HISAT and TopHat2, both of which are spliced alignment
>+program for mapping RNA-seq reads; additionally, HISAT2 is designed to map
>+sequencing reads from genomic DNA of generic human population having SNPs.
>+
>+Citation:
>+Kim et al. (2015) HISAT: a fast spliced aligner with low memory requirements.
>+Nature Methods 12: 357-360.
>+
>+WWW: https://ccb.jhu.edu/software/hisat2/
>
>Property changes on: pkg-descr
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(nonexistent)
>+++ pkg-plist	(working copy)
>@@ -0,0 +1,15 @@
>+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
>
>Property changes on: pkg-plist
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 229330: 194628