Attachment #187512 for bug #223273




# $FreeBSD$

PORTNAME=	ngs
PORTVERSION=	1.3.0
CATEGORIES=	biology
PKGNAMESUFFIX=	-sdk

MAINTAINER=	mzaki@niid.go.jp
COMMENT=	NCBI's front-end API for NGS data manipulation

LICENSE=	PD
LICENSE_FILE=	${WRKSRC}/../LICENSE

USE_GITHUB=	yes
GH_ACCOUNT=	ncbi

USES=		compiler gmake perl5
USE_PERL5=	build
GNU_CONFIGURE=	yes
CONFIGURE_ARGS=	CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
USE_LDCONFIG=	yes

WRKSRC_SUBDIR=	ngs-sdk
ALL_TARGET=	subtargs

# for port developpers, building with these options may fail
OPTIONS_DEFINE=	EXAMPLES GCC DEBUG OPTIMIZED_CFLAGS TEST
DEBUG_PREVENTS=	OPTIMIZED_CFLAGS
DEBUG_CONFIGURE_WITH=	debug
GCC_USE=	gcc=yes
OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
TEST_TEST_TARGET=	test

post-build-TEST-on:	do-test

do-install:
	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copylibs copyincludes)

post-install-EXAMPLES-on:
	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copyexamples)

.include <bsd.port.mk>

Line 0 Link Here

(-)biology/ngs-sdk/distinfo (+3 lines)
	1	TIMESTAMP = 1504850804
	2	SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2
	3	SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187




--- Makefile.install.orig	2016-10-07 21:59:36 UTC
+++ Makefile.install
@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \
     ngs-c++.$(VERSION_LIBX) \
     ngs-adapt-c++.$(VERSION_LIBX) \
 
-LIB_TARGET = $(INST_LIBDIR)$(BITS)
+LIB_TARGET = $(INST_LIBDIR)
 
 LIBRARIES_WITH_PREFIX = \
 	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
@@ -53,8 +53,8 @@ copyincludes:
 
 copyexamples:
 	@ echo "Installing examples to $(INST_SHAREDIR)"
-	@ mkdir -p $(INST_SHAREDIR)/examples
-	@ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples
+	@ mkdir -p $(INST_SHAREDIR)/examples/ngs
+	@ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples/ngs
 
 #fake root for debugging
 #uncomment this line and change the test for root ( see under install: ) to succeed:

Line 0 Link Here

(-)biology/ngs-sdk/files/patch-Makefile.libs (+11 lines)
	1	--- Makefile.libs.orig 2016-10-07 21:59:36 UTC
	2	+++ Makefile.libs
	3	@@ -109,7 +109,7 @@ SDK_DEPS = \
	4	$(ILIBDIR)/$(LPFX)ngs-disp.$(LIBX)
	5
	6	$(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX): $(SDK_DEPS)
	7	- $(LP) $(DBG) $(OPT) -shared -o $@ $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB)
	8	+ $(LP) $(DBG) $(OPT) -shared -o $@ $(LDFLAGS) $(SONAME) `cat $(addsuffix /manifest,$(SDK_XLIBS))` $(SDK_LIB)
	9
	10	$(LIBDIR)/$(LPFX)ngs-sdk.$(MAJVERS_SHLX): $(LIBDIR)/$(LPFX)ngs-sdk.$(VERSION_SHLX)
	11	rm -f $@




--- setup/konfigure.perl.orig	2016-10-07 21:59:36 UTC
+++ setup/konfigure.perl
@@ -186,7 +186,7 @@ if ($OPT{'help'}) {
 foreach (@ARGV) {
     @_ = split('=');
     next if ($#_ != 1);
-    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS');
+    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS');
 }
 
 println "Configuring $PACKAGE_NAME package";
@@ -198,7 +198,7 @@ print "checking system type... " unless 
 my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
 println $OSTYPE unless ($AUTORUN);
 
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
     println "configure: error: unsupported system '$OSTYPE'";
     exit 1;
 }
@@ -213,7 +213,7 @@ if ($OS eq 'linux') {
 
 print "checking machine architecture... " unless ($AUTORUN);
 println $MARCH unless ($AUTORUN);
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) {
     println "configure: error: unsupported architecture '$OSTYPE'";
     exit 1;
 }
@@ -298,7 +298,7 @@ print "checking for supported architectu
 
 my $BITS;
 
-if ($MARCH =~ /x86_64/i) {
+if ($MARCH =~ /(x86_|amd)64/i) {
     $BITS = 64;
 } elsif ($MARCH eq 'fat86') {
     $BITS = '32_64';
@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) {
     $EXEX = '';
     $OSINC = 'unix';
     $TOOLS = 'clang' unless ($TOOLS);
+} elsif ($OSTYPE =~ /freebsd/i) {
+    $LPFX = 'lib';
+    $OBJX = 'o';
+    $LOBX = 'pic.o';
+    $LIBX = 'a';
+    $SHLX = 'so';
+    $EXEX = '';
+    $OSINC = 'unix';
+    unless ($TOOLS) {
+        $TOOLS = 'clang';
+        $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
+    }
 } elsif ($OSTYPE eq 'win') {
     $TOOLS = 'vc++';
 } else {
@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M
 
 print "checking for supported tool chain... " unless ($AUTORUN);
 
+$CC      = $OPT{CC     } if ($OPT{CC     });
 $CPP     = $OPT{CXX    } if ($OPT{CXX    });
 $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
 
 if ($TOOLS =~ /gcc$/) {
     $CPP  = 'g++' unless ($CPP);
-    $CC   = "$TOOLS -c";
+    $CC   = 'gcc' unless ($CC);
+    $LD   = $CC;
+    $CC   = "$CC -c";
     $CP   = "$CPP -c";
     $AR   = 'ar rc';
     $ARX  = 'ar x';
     $ARLS = 'ar t';
-    $LD   = $TOOLS;
     $LP   = $CPP;
 
     $DBG = '-g -DDEBUG';
@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) {
     $MD  = '-MD';
 } elsif ($TOOLS eq 'clang') {
     $CPP  = 'clang++' unless ($CPP);
-    $CC   = 'clang -c';
-    my $versionMin = '-mmacosx-version-min=10.6';
+    $CC   = 'clang' unless ($CC);
+    $LD   = $CC;
+    $CC   = "$CC -c";
+    my $versionMin = '';
+    $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
     $CP   = "$CPP -c $versionMin";
     if ($BITS ne '32_64') {
-        $ARCH_FL = '-arch i386' if ($BITS == 32);
+        $ARCH_FL = '-arch i386' if ($OSTYPE =~ /darwin/i && $BITS == 32);
         $OPT = '-O3';
         $AR      = 'ar rc';
-        $LD      = "clang $ARCH_FL";
+        $LD      = "$LD $ARCH_FL";
         $LP      = "$CPP $versionMin $ARCH_FL";
     } else {
         $MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
         $ARCH_FL       = '-arch i386 -arch x86_64';
         $OPT    = '-O3';
         $AR     = 'libtool -static -o';
-        $LD     = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
+        $LD     = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
         $LP     = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
     }
     $ARX  = 'ar x';
@@ -755,13 +772,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os
 # install paths
 EndText
 
-    L($F, "INST_BINDIR = $OPT{'bindir'}"      ) if ($OPT{'bindir'});
-    L($F, "INST_LIBDIR = $OPT{'libdir'}"      ) if ($OPT{'libdir'});
-    L($F, "INST_INCDIR = $OPT{'includedir'}"  ) if ($OPT{'includedir'});
-    L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
-    L($F, "INST_SHAREDIR = $OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
-    L($F, "INST_JARDIR = $OPT{'javadir'}"     ) if ($OPT{'javadir'});
-    L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
+    L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}"      ) if ($OPT{'bindir'});
+    L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}"      ) if ($OPT{'libdir'});
+    L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}"  ) if ($OPT{'includedir'});
+    L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
+    L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
+    L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}"     ) if ($OPT{'javadir'});
+    L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
 
     my ($E_VERSION_SHLX, $VERSION_SHLX,
         $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
@@ -825,7 +842,7 @@ MAJMIN_EXEX  = \$(EXEX).\$(MAJMIN)
 MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
 
 # system architecture and wordsize
-ARCH = $ARCH
+override ARCH = $ARCH
 EndText
 
     L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
@@ -860,7 +877,7 @@ EndText
     }
     L($F, "PIC     = $PIC") if ($PIC);
     if ($PKG{LNG} eq 'C') {
-        if ($TOOLS =~ /clang/i) {
+        if ($OSTYPE =~ /darwin/i) {
    L($F, 'SONAME  = -install_name ' .
                '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
@@ -884,7 +901,7 @@ EndText
         }
     }
     if ($PKG{LNG} eq 'C') {
-        L($F, "CFLAGS  = \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
+        L($F, "CFLAGS  += \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
     }
     L($F, "LDFLAGS = $LDFLAGS") if ($LDFLAGS);
 
@@ -970,7 +987,7 @@ EndText
     L($F, '# directory rules');
     if ($PKG{LNG} eq 'C') {
         L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
-            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
+            . '$(OBJDIR) $(INST_LIBDIR):');
         T($F, 'mkdir -p $@');
     } elsif ($PKG{LNG} eq 'JAVA') {
         # test if we have jni header path
@@ -1000,12 +1017,12 @@ EndText
     L($F, 'export CONFIGURE_FOUND_XML2');
     L($F);
 
-    if ($OS eq 'linux' || $OS eq 'mac') {
+    if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') {
         L($F, '# installation rules');
         L($F,
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
+        '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
         T($F, '@ echo -n "installing \'$(@F)\'... "');
-        T($F, '@ if cp $^ $@ && chmod 644 $@;                         \\');
+        T($F, '@ if $(BSD_INSTALL_DATA) $^ $@;                        \\');
         T($F, '  then                                                 \\');
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
                      . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
@@ -1014,7 +1031,7 @@ EndText
         T($F, '      ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
                       . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
         T($F, '      ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
-   '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
+   '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
                                                               . ' \\');
         T($F, '      echo success;                                    \\');
         T($F, '  else                                                 \\');
@@ -1024,15 +1041,15 @@ EndText
         L($F);
 
         L($F,
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
+        '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
         T($F, '@ echo -n "installing \'$(@F)\'... "');
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
+        T($F, '@ if $(BSD_INSTALL_LIB) $^ $@;                         \\');
         T($F, '  then                                                 \\');
         if ($OS ne 'mac') {
           T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
                       . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@);    \\');
         }
-        if ($OS eq 'linux') {
+        if ($OS eq 'linux' || $OS eq 'bsd') {
           T($F, '      ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
         } elsif ($OS eq 'mac') {
           T($F, '      ln -sf $(@F) '
@@ -1051,7 +1068,7 @@ EndText
 
         L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
         T($F, '@ echo -n "installing \'$(@F)\'... "');
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
+        T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@;                     \\');
         T($F, '  then                                                 \\');
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
                       . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@);     \\');
@@ -1333,7 +1350,7 @@ sub find_in_dir {
                 ++$found;
             }
             if (! $found) {
-                my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
+                my $libdir = File::Spec->catdir($dir, 'lib');
                 my $f = File::Spec->catdir($libdir, $lib);
                 print "\tchecking $f\n\t" if ($OPT{'debug'});
                 if (-e $f) {




--- setup/os-arch.prl.orig	2016-10-07 21:59:36 UTC
+++ setup/os-arch.prl
@@ -11,6 +11,8 @@ sub OsArch {
         chomp $UNAME;
         if ($UNAME =~ /Darwin/) {
             $HOST_OS = 'mac';
+        } elsif ($UNAME =~ /.*BSD/) {
+            $HOST_OS = 'bsd';
         } elsif ($UNAME =~ /Linux/) {
             $HOST_OS = 'linux';
         } elsif ($UNAME =~ /SunOS/) {
@@ -49,6 +51,8 @@ sub OsArch {
                 }
             } elsif ($MARCH =~ /x86_64/) {
                 $HOST_ARCH = 'x86_64';
+            } elsif ($MARCH =~ /amd64/) {
+                $HOST_ARCH = 'x86_64';
             } elsif ($MARCH =~ /i86pc/) {
                 $HOST_ARCH = 'x86_64';
                 @ARCHITECTURES = qw(x86_64 i386);




NGS is NCBI's 'front-end' API for accessing reads, alignments and pileups
produced from Next Generation Sequencing. The 'back-end' engine are provided
by biology/ncbi-vdb port.

Although the GitHub repository contains C++, Java and Python libraries,
this port only install the following libraries to simplify dependencies.

libngs-c++.a       C++ front-end API
libngs-adapt-c++.a C++ adapter for C-based protocol to back-end engine
libngs-sdk.so      Java and Python language bindings of the front-end API

See ${WRKSRC}/CONTENTS for the detail.

WWW: https://github.com/ncbi/ngs/wiki




include/ngs/Alignment.hpp
include/ngs/AlignmentIterator.hpp
include/ngs/ErrorMsg.hpp
include/ngs/Fragment.hpp
include/ngs/FragmentIterator.hpp
include/ngs/Package.hpp
include/ngs/Pileup.hpp
include/ngs/PileupEvent.hpp
include/ngs/PileupEventIterator.hpp
include/ngs/PileupIterator.hpp
include/ngs/Read.hpp
include/ngs/ReadCollection.hpp
include/ngs/ReadGroup.hpp
include/ngs/ReadGroupIterator.hpp
include/ngs/ReadIterator.hpp
include/ngs/Reference.hpp
include/ngs/ReferenceIterator.hpp
include/ngs/ReferenceSequence.hpp
include/ngs/Statistics.hpp
include/ngs/StringRef.hpp
include/ngs/adapter/AlignmentItf.hpp
include/ngs/adapter/ErrorMsg.hpp
include/ngs/adapter/FragmentItf.hpp
include/ngs/adapter/PileupEventItf.hpp
include/ngs/adapter/PileupItf.hpp
include/ngs/adapter/ReadCollectionItf.hpp
include/ngs/adapter/ReadGroupItf.hpp
include/ngs/adapter/ReadItf.hpp
include/ngs/adapter/Refcount.hpp
include/ngs/adapter/ReferenceItf.hpp
include/ngs/adapter/ReferenceSequenceItf.hpp
include/ngs/adapter/StatisticsItf.hpp
include/ngs/adapter/StringItf.hpp
include/ngs/adapter/defs.h
include/ngs/inl/Alignment.hpp
include/ngs/inl/AlignmentIterator.hpp
include/ngs/inl/Fragment.hpp
include/ngs/inl/FragmentIterator.hpp
include/ngs/inl/Package.hpp
include/ngs/inl/Pileup.hpp
include/ngs/inl/PileupEvent.hpp
include/ngs/inl/PileupEventIterator.hpp
include/ngs/inl/PileupIterator.hpp
include/ngs/inl/Read.hpp
include/ngs/inl/ReadCollection.hpp
include/ngs/inl/ReadGroup.hpp
include/ngs/inl/ReadGroupIterator.hpp
include/ngs/inl/ReadIterator.hpp
include/ngs/inl/Reference.hpp
include/ngs/inl/ReferenceIterator.hpp
include/ngs/inl/ReferenceSequence.hpp
include/ngs/inl/Statistics.hpp
include/ngs/inl/StringRef.hpp
include/ngs/itf/AlignmentItf.h
include/ngs/itf/AlignmentItf.hpp
include/ngs/itf/ErrBlock.h
include/ngs/itf/ErrBlock.hpp
include/ngs/itf/ErrorMsg.hpp
include/ngs/itf/FragmentItf.h
include/ngs/itf/FragmentItf.hpp
include/ngs/itf/PackageItf.hpp
include/ngs/itf/PileupEventItf.h
include/ngs/itf/PileupEventItf.hpp
include/ngs/itf/PileupItf.h
include/ngs/itf/PileupItf.hpp
include/ngs/itf/ReadCollectionItf.h
include/ngs/itf/ReadCollectionItf.hpp
include/ngs/itf/ReadGroupItf.h
include/ngs/itf/ReadGroupItf.hpp
include/ngs/itf/ReadItf.h
include/ngs/itf/ReadItf.hpp
include/ngs/itf/Refcount.h
include/ngs/itf/Refcount.hpp
include/ngs/itf/ReferenceItf.h
include/ngs/itf/ReferenceItf.hpp
include/ngs/itf/ReferenceSequenceItf.h
include/ngs/itf/ReferenceSequenceItf.hpp
include/ngs/itf/StatisticsItf.h
include/ngs/itf/StatisticsItf.hpp
include/ngs/itf/StringItf.h
include/ngs/itf/StringItf.hpp
include/ngs/itf/VTable.h
include/ngs/itf/VTable.hpp
include/ngs/itf/defs.h
include/ngs/unix/fat86/atomic32.h
include/ngs/unix/i386/atomic32.h
include/ngs/unix/x86_64/atomic32.h
include/ngs/win/atomic32.h
include/ngs/win/stdbool.h
lib/libngs-adapt-c++-static.a
lib/libngs-adapt-c++.a
lib/libngs-adapt-c++.a.1
lib/libngs-adapt-c++.a.1.3.0
lib/libngs-c++-static.a
lib/libngs-c++.a
lib/libngs-c++.a.1
lib/libngs-c++.a.1.3.0
lib/libngs-sdk.so
lib/libngs-sdk.so.1
lib/libngs-sdk.so.1.3.0
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FastqTableDump.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.config
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp

Return to bug 223273

Line 0 Link Here

(-)biology/ngs-sdk/Makefile (+42 lines)
	1	# $FreeBSD$
	2
	3	PORTNAME= ngs
	4	PORTVERSION= 1.3.0
	5	CATEGORIES= biology
	6	PKGNAMESUFFIX= -sdk
	7
	8	MAINTAINER= mzaki@niid.go.jp
	9	COMMENT= NCBI's front-end API for NGS data manipulation
	10
	11	LICENSE= PD
	12	LICENSE_FILE= ${WRKSRC}/../LICENSE
	13
	14	USE_GITHUB= yes
	15	GH_ACCOUNT= ncbi
	16
	17	USES= compiler gmake perl5
	18	USE_PERL5= build
	19	GNU_CONFIGURE= yes
	20	CONFIGURE_ARGS= CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
	21	USE_LDCONFIG= yes
	22
	23	WRKSRC_SUBDIR= ngs-sdk
	24	ALL_TARGET= subtargs
	25
	26	# for port developpers, building with these options may fail
	27	OPTIONS_DEFINE= EXAMPLES GCC DEBUG OPTIMIZED_CFLAGS TEST
	28	DEBUG_PREVENTS= OPTIMIZED_CFLAGS
	29	DEBUG_CONFIGURE_WITH= debug
	30	GCC_USE= gcc=yes
	31	OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT=""
	32	TEST_TEST_TARGET= test
	33
	34	post-build-TEST-on: do-test
	35
	36	do-install:
	37	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copylibs copyincludes)
	38
	39	post-install-EXAMPLES-on:
	40	@(cd ${INSTALL_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f Makefile.install ${MAKE_ARGS} copyexamples)
	41
	42	.include <bsd.port.mk>

Line 0 Link Here

(-)biology/ngs-sdk/files/patch-Makefile.install (+22 lines)
	1	--- Makefile.install.orig 2016-10-07 21:59:36 UTC
	2	+++ Makefile.install
	3	@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \
	4	ngs-c++.$(VERSION_LIBX) \
	5	ngs-adapt-c++.$(VERSION_LIBX) \
	6
	7	-LIB_TARGET = $(INST_LIBDIR)$(BITS)
	8	+LIB_TARGET = $(INST_LIBDIR)
	9
	10	LIBRARIES_WITH_PREFIX = \
	11	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
	12	@@ -53,8 +53,8 @@ copyincludes:
	13
	14	copyexamples:
	15	@ echo "Installing examples to $(INST_SHAREDIR)"
	16	- @ mkdir -p $(INST_SHAREDIR)/examples
	17	- @ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples
	18	+ @ mkdir -p $(INST_SHAREDIR)/examples/ngs
	19	+ @ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples/ngs
	20
	21	#fake root for debugging
	22	#uncomment this line and change the test for root ( see under install: ) to succeed:

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(-)biology/ngs-sdk/files/patch-setup_konfigure.perl (+228 lines)
		1	--- setup/konfigure.perl.orig 2016-10-07 21:59:36 UTC
		2	+++ setup/konfigure.perl
		3	@@ -186,7 +186,7 @@ if ($OPT{'help'}) {
		4	foreach (@ARGV) {
		5	@_ = split('=');
		6	next if ($#_ != 1);
		7	- $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' \|\| $_[0] eq 'LDFLAGS');
		8	+ $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' \|\| $_[0] eq 'CXX' \|\| $_[0] eq 'LDFLAGS' \|\| $_[0] eq 'TOOLS');
		9	}
		10
		11	println "Configuring $PACKAGE_NAME package";
		12	@@ -198,7 +198,7 @@ print "checking system type... " unless
		13	my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
		14	println $OSTYPE unless ($AUTORUN);
		15
		16	-unless ($OSTYPE =~ /linux/i \|\| $OSTYPE =~ /darwin/i \|\| $OSTYPE eq 'win') {
		17	+unless ($OSTYPE =~ /linux/i \|\| $OSTYPE =~ /freebsd/i \|\| $OSTYPE =~ /darwin/i \|\| $OSTYPE eq 'win') {
		18	println "configure: error: unsupported system '$OSTYPE'";
		19	exit 1;
		20	}
		21	@@ -213,7 +213,7 @@ if ($OS eq 'linux') {
		22
		23	print "checking machine architecture... " unless ($AUTORUN);
		24	println $MARCH unless ($AUTORUN);
		25	-unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /i?86/i) {
		26	+unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /amd64/i \|\| $MARCH =~ /i?86/i) {
		27	println "configure: error: unsupported architecture '$OSTYPE'";
		28	exit 1;
		29	}
		30	@@ -298,7 +298,7 @@ print "checking for supported architectu
		31
		32	my $BITS;
		33
		34	-if ($MARCH =~ /x86_64/i) {
		35	+if ($MARCH =~ /(x86_\|amd)64/i) {
		36	$BITS = 64;
		37	} elsif ($MARCH eq 'fat86') {
		38	$BITS = '32_64';
		39	@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) {
		40	$EXEX = '';
		41	$OSINC = 'unix';
		42	$TOOLS = 'clang' unless ($TOOLS);
		43	+} elsif ($OSTYPE =~ /freebsd/i) {
		44	+ $LPFX = 'lib';
		45	+ $OBJX = 'o';
		46	+ $LOBX = 'pic.o';
		47	+ $LIBX = 'a';
		48	+ $SHLX = 'so';
		49	+ $EXEX = '';
		50	+ $OSINC = 'unix';
		51	+ unless ($TOOLS) {
		52	+ $TOOLS = 'clang';
		53	+ $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
		54	+ }
		55	} elsif ($OSTYPE eq 'win') {
		56	$TOOLS = 'vc++';
		57	} else {
		58	@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M
		59
		60	print "checking for supported tool chain... " unless ($AUTORUN);
		61
		62	+$CC = $OPT{CC } if ($OPT{CC });
		63	$CPP = $OPT{CXX } if ($OPT{CXX });
		64	$LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
65
66	if ($TOOLS =~ /gcc$/) {
67	$CPP = 'g++' unless ($CPP);
68	- $CC = "$TOOLS -c";
69	+ $CC = 'gcc' unless ($CC);
70	+ $LD = $CC;
71	+ $CC = "$CC -c";
72	$CP = "$CPP -c";
73	$AR = 'ar rc';
74	$ARX = 'ar x';
75	$ARLS = 'ar t';
76	- $LD = $TOOLS;
77	$LP = $CPP;
78
79	$DBG = '-g -DDEBUG';
80	@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) {
81	$MD = '-MD';
82	} elsif ($TOOLS eq 'clang') {
83	$CPP = 'clang++' unless ($CPP);
84	- $CC = 'clang -c';
85	- my $versionMin = '-mmacosx-version-min=10.6';
86	+ $CC = 'clang' unless ($CC);
87	+ $LD = $CC;
88	+ $CC = "$CC -c";
89	+ my $versionMin = '';
90	+ $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
91	$CP = "$CPP -c $versionMin";
92	if ($BITS ne '32_64') {
93	- $ARCH_FL = '-arch i386' if ($BITS == 32);
94	+ $ARCH_FL = '-arch i386' if ($OSTYPE =~ /darwin/i && $BITS == 32);
95	$OPT = '-O3';
96	$AR = 'ar rc';
97	- $LD = "clang $ARCH_FL";
98	+ $LD = "$LD $ARCH_FL";
99	$LP = "$CPP $versionMin $ARCH_FL";
100	} else {
101	$MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
102	$ARCH_FL = '-arch i386 -arch x86_64';
103	$OPT = '-O3';
104	$AR = 'libtool -static -o';
105	- $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
106	+ $LD = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
107	$LP = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
108	}
109	$ARX = 'ar x';
110	@@ -755,13 +772,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os
111	# install paths
112	EndText
113
114	- L($F, "INST_BINDIR = $OPT{'bindir'}" ) if ($OPT{'bindir'});
115	- L($F, "INST_LIBDIR = $OPT{'libdir'}" ) if ($OPT{'libdir'});
116	- L($F, "INST_INCDIR = $OPT{'includedir'}" ) if ($OPT{'includedir'});
117	- L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
118	- L($F, "INST_SHAREDIR = $OPT{'sharedir'}" ) if ($OPT{'sharedir'});
119	- L($F, "INST_JARDIR = $OPT{'javadir'}" ) if ($OPT{'javadir'});
120	- L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
121	+ L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}" ) if ($OPT{'bindir'});
122	+ L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}" ) if ($OPT{'libdir'});
123	+ L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}" ) if ($OPT{'includedir'});
124	+ L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
125	+ L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}" ) if ($OPT{'sharedir'});
126	+ L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}" ) if ($OPT{'javadir'});
127	+ L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
128
129	my ($E_VERSION_SHLX, $VERSION_SHLX,
130	$E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
131	@@ -825,7 +842,7 @@ MAJMIN_EXEX = \$(EXEX).\$(MAJMIN)
132	MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
133
134	# system architecture and wordsize
135	-ARCH = $ARCH
136	+override ARCH = $ARCH
137	EndText
138
139	L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
140	@@ -860,7 +877,7 @@ EndText
141	}
142	L($F, "PIC = $PIC") if ($PIC);
143	if ($PKG{LNG} eq 'C') {
144	- if ($TOOLS =~ /clang/i) {
145	+ if ($OSTYPE =~ /darwin/i) {
146	L($F, 'SONAME = -install_name ' .
147	'$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
148	L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
149	@@ -884,7 +901,7 @@ EndText
150	}
151	}
152	if ($PKG{LNG} eq 'C') {
153	- L($F, "CFLAGS = \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
154	+ L($F, "CFLAGS += \$(DBG) \$(OPT) \$(INCDIRS) $MD $ARCH_FL");
155	}
156	L($F, "LDFLAGS = $LDFLAGS") if ($LDFLAGS);
157
158	@@ -970,7 +987,7 @@ EndText
159	L($F, '# directory rules');
160	if ($PKG{LNG} eq 'C') {
161	L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
162	- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
163	+ . '$(OBJDIR) $(INST_LIBDIR):');
164	T($F, 'mkdir -p $@');
165	} elsif ($PKG{LNG} eq 'JAVA') {
166	# test if we have jni header path
167	@@ -1000,12 +1017,12 @@ EndText
168	L($F, 'export CONFIGURE_FOUND_XML2');
169	L($F);
170
171	- if ($OS eq 'linux' \|\| $OS eq 'mac') {
172	+ if ($OS eq 'linux' \|\| $OS eq 'bsd' \|\| $OS eq 'mac') {
173	L($F, '# installation rules');
174	L($F,
175	- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
176	+ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
177	T($F, '@ echo -n "installing \'$(@F)\'... "');
178	- T($F, '@ if cp $^ $@ && chmod 644 $@; \\');
179	+ T($F, '@ if $(BSD_INSTALL_DATA) $^ $@; \\');
180	T($F, ' then \\');
181	T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
182	. '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
183	@@ -1014,7 +1031,7 @@ EndText
184	T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
185	. '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
186	T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
187	- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
188	+ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
189	. ' \\');
190	T($F, ' echo success; \\');
191	T($F, ' else \\');
192	@@ -1024,15 +1041,15 @@ EndText
193	L($F);
194
195	L($F,
196	- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
197	+ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
198	T($F, '@ echo -n "installing \'$(@F)\'... "');
199	- T($F, '@ if cp $^ $@ && chmod 755 $@; \\');
200	+ T($F, '@ if $(BSD_INSTALL_LIB) $^ $@; \\');
201	T($F, ' then \\');
202	if ($OS ne 'mac') {
203	T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
204	. '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@); \\');
205	}
206	- if ($OS eq 'linux') {
207	+ if ($OS eq 'linux' \|\| $OS eq 'bsd') {
208	T($F, ' ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
209	} elsif ($OS eq 'mac') {
210	T($F, ' ln -sf $(@F) '
211	@@ -1051,7 +1068,7 @@ EndText
212
213	L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
214	T($F, '@ echo -n "installing \'$(@F)\'... "');
215	- T($F, '@ if cp $^ $@ && chmod 755 $@; \\');
216	+ T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@; \\');
217	T($F, ' then \\');
218	T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
219	. '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@); \\');
220	@@ -1333,7 +1350,7 @@ sub find_in_dir {
221	++$found;
222	}
223	if (! $found) {
224	- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
225	+ my $libdir = File::Spec->catdir($dir, 'lib');
226	my $f = File::Spec->catdir($libdir, $lib);
227	print "\tchecking $f\n\t" if ($OPT{'debug'});
228	if (-e $f) {

Line 0 Link Here

(-)biology/ngs-sdk/files/patch-setup_os-arch.prl (+20 lines)
	1	--- setup/os-arch.prl.orig 2016-10-07 21:59:36 UTC
	2	+++ setup/os-arch.prl
	3	@@ -11,6 +11,8 @@ sub OsArch {
	4	chomp $UNAME;
	5	if ($UNAME =~ /Darwin/) {
	6	$HOST_OS = 'mac';
	7	+ } elsif ($UNAME =~ /.*BSD/) {
	8	+ $HOST_OS = 'bsd';
	9	} elsif ($UNAME =~ /Linux/) {
	10	$HOST_OS = 'linux';
	11	} elsif ($UNAME =~ /SunOS/) {
	12	@@ -49,6 +51,8 @@ sub OsArch {
	13	}
	14	} elsif ($MARCH =~ /x86_64/) {
	15	$HOST_ARCH = 'x86_64';
	16	+ } elsif ($MARCH =~ /amd64/) {
	17	+ $HOST_ARCH = 'x86_64';
	18	} elsif ($MARCH =~ /i86pc/) {
	19	$HOST_ARCH = 'x86_64';
	20	@ARCHITECTURES = qw(x86_64 i386);

Line 0 Link Here

(-)biology/ngs-sdk/pkg-descr (+14 lines)
	1	NGS is NCBI's 'front-end' API for accessing reads, alignments and pileups
	2	produced from Next Generation Sequencing. The 'back-end' engine are provided
	3	by biology/ncbi-vdb port.
	4
	5	Although the GitHub repository contains C++, Java and Python libraries,
	6	this port only install the following libraries to simplify dependencies.
	7
	8	libngs-c++.a C++ front-end API
	9	libngs-adapt-c++.a C++ adapter for C-based protocol to back-end engine
	10	libngs-sdk.so Java and Python language bindings of the front-end API
	11
	12	See ${WRKSRC}/CONTENTS for the detail.
	13
	14	WWW: https://github.com/ncbi/ngs/wiki

Line 0 Link Here

(-)biology/ngs-sdk/pkg-plist (+109 lines)
		1	include/ngs/Alignment.hpp
		2	include/ngs/AlignmentIterator.hpp
		3	include/ngs/ErrorMsg.hpp
		4	include/ngs/Fragment.hpp
		5	include/ngs/FragmentIterator.hpp
		6	include/ngs/Package.hpp
		7	include/ngs/Pileup.hpp
		8	include/ngs/PileupEvent.hpp
		9	include/ngs/PileupEventIterator.hpp
		10	include/ngs/PileupIterator.hpp
		11	include/ngs/Read.hpp
		12	include/ngs/ReadCollection.hpp
		13	include/ngs/ReadGroup.hpp
		14	include/ngs/ReadGroupIterator.hpp
		15	include/ngs/ReadIterator.hpp
		16	include/ngs/Reference.hpp
		17	include/ngs/ReferenceIterator.hpp
		18	include/ngs/ReferenceSequence.hpp
		19	include/ngs/Statistics.hpp
		20	include/ngs/StringRef.hpp
		21	include/ngs/adapter/AlignmentItf.hpp
		22	include/ngs/adapter/ErrorMsg.hpp
		23	include/ngs/adapter/FragmentItf.hpp
		24	include/ngs/adapter/PileupEventItf.hpp
		25	include/ngs/adapter/PileupItf.hpp
		26	include/ngs/adapter/ReadCollectionItf.hpp
		27	include/ngs/adapter/ReadGroupItf.hpp
		28	include/ngs/adapter/ReadItf.hpp
		29	include/ngs/adapter/Refcount.hpp
		30	include/ngs/adapter/ReferenceItf.hpp
		31	include/ngs/adapter/ReferenceSequenceItf.hpp
		32	include/ngs/adapter/StatisticsItf.hpp
		33	include/ngs/adapter/StringItf.hpp
		34	include/ngs/adapter/defs.h
		35	include/ngs/inl/Alignment.hpp
		36	include/ngs/inl/AlignmentIterator.hpp
		37	include/ngs/inl/Fragment.hpp
		38	include/ngs/inl/FragmentIterator.hpp
		39	include/ngs/inl/Package.hpp
		40	include/ngs/inl/Pileup.hpp
		41	include/ngs/inl/PileupEvent.hpp
		42	include/ngs/inl/PileupEventIterator.hpp
		43	include/ngs/inl/PileupIterator.hpp
		44	include/ngs/inl/Read.hpp
		45	include/ngs/inl/ReadCollection.hpp
		46	include/ngs/inl/ReadGroup.hpp
		47	include/ngs/inl/ReadGroupIterator.hpp
		48	include/ngs/inl/ReadIterator.hpp
		49	include/ngs/inl/Reference.hpp
		50	include/ngs/inl/ReferenceIterator.hpp
		51	include/ngs/inl/ReferenceSequence.hpp
		52	include/ngs/inl/Statistics.hpp
		53	include/ngs/inl/StringRef.hpp
		54	include/ngs/itf/AlignmentItf.h
		55	include/ngs/itf/AlignmentItf.hpp
		56	include/ngs/itf/ErrBlock.h
		57	include/ngs/itf/ErrBlock.hpp
		58	include/ngs/itf/ErrorMsg.hpp
		59	include/ngs/itf/FragmentItf.h
		60	include/ngs/itf/FragmentItf.hpp
		61	include/ngs/itf/PackageItf.hpp
		62	include/ngs/itf/PileupEventItf.h
		63	include/ngs/itf/PileupEventItf.hpp
		64	include/ngs/itf/PileupItf.h
65	include/ngs/itf/PileupItf.hpp
66	include/ngs/itf/ReadCollectionItf.h
67	include/ngs/itf/ReadCollectionItf.hpp
68	include/ngs/itf/ReadGroupItf.h
69	include/ngs/itf/ReadGroupItf.hpp
70	include/ngs/itf/ReadItf.h
71	include/ngs/itf/ReadItf.hpp
72	include/ngs/itf/Refcount.h
73	include/ngs/itf/Refcount.hpp
74	include/ngs/itf/ReferenceItf.h
75	include/ngs/itf/ReferenceItf.hpp
76	include/ngs/itf/ReferenceSequenceItf.h
77	include/ngs/itf/ReferenceSequenceItf.hpp
78	include/ngs/itf/StatisticsItf.h
79	include/ngs/itf/StatisticsItf.hpp
80	include/ngs/itf/StringItf.h
81	include/ngs/itf/StringItf.hpp
82	include/ngs/itf/VTable.h
83	include/ngs/itf/VTable.hpp
84	include/ngs/itf/defs.h
85	include/ngs/unix/fat86/atomic32.h
86	include/ngs/unix/i386/atomic32.h
87	include/ngs/unix/x86_64/atomic32.h
88	include/ngs/win/atomic32.h
89	include/ngs/win/stdbool.h
90	lib/libngs-adapt-c++-static.a
91	lib/libngs-adapt-c++.a
92	lib/libngs-adapt-c++.a.1
93	lib/libngs-adapt-c++.a.1.3.0
94	lib/libngs-c++-static.a
95	lib/libngs-c++.a
96	lib/libngs-c++.a.1
97	lib/libngs-c++.a.1.3.0
98	lib/libngs-sdk.so
99	lib/libngs-sdk.so.1
100	lib/libngs-sdk.so.1.3.0
101	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
102	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
103	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
104	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FastqTableDump.cpp
105	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
106	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
107	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.config
108	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
109	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp