# $FreeBSD$

PORTNAME=	ncbi-vdb

DISTVERSION=	2.8.2-2

CATEGORIES=	biology

MAINTAINER=	mzaki@niid.go.jp

COMMENT=	NCBI's virtualized back-end for accessing Sequence Read Archive

LICENSE=	PD LGPL21+

LICENSE_COMB=	multi

LICENSE_FILE_PD=	${WRKSRC}/LICENSE

LICENSE_DISTFILES_LGPL21+ =	${DISTNAME}${EXTRACT_SUFX}

# This port never use the bundled libraries otherwise licensed.

BUILD_DEPENDS=	bash:shells/bash

LIB_DEPENDS=	libxml2.so:textproc/libxml2 \

		libhdf5.so:science/hdf5 \

		libmbedtls.so:security/mbedtls

USE_GITHUB=	yes

GH_ACCOUNT=	ncbi

GH_TUPLE+=	ncbi:ngs:1.3.0:ngs

USES=		compiler gmake perl5 shebangfix

USE_PERL5=	build

SHEBANG_GLOB=	*.sh *.pl

GNU_CONFIGURE=	yes

CONFIGURE_ARGS=	--with-xml2-prefix=${LOCALBASE} \

		--with-hdf5-prefix=${LOCALBASE} \

		--with-mbedtls-prefix=${LOCALBASE} \

		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"

MAKE_ARGS+=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"

USE_LDCONFIG=	yes

MAKE_JOBS_UNSAFE=	yes

ONLY_FOR_ARCHS=	amd64 i386

ONLY_FOR_ARCHS_REASON=	libs/search/nucstrstr.c requires SSE2 instructions

# for port developpers, building with these options may fail

OPTIONS_DEFINE=	DEBUG GCC 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-extract:

	@${LN} -sf ${WRKSRC_ngs} ${WRKDIR}/ngs

	@${LN} -sf ${WRKSRC} ${WRKDIR}/${PORTNAME}

pre-patch:

	@${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/

	@for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done

	@${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh

	@${MKDIR} ${WRKSRC}/interfaces/os/bsd

	@${CP} -p ${WRKSRC}/interfaces/os/mac/endian.h ${WRKSRC}/interfaces/os/bsd/

	@${REINPLACE_CMD} -e 's/vdb_mbedtls_/mbedtls_/g' ${WRKSRC}/libs/kns/tls.c

	@${RM} -rf ${WRKSRC}/interfaces/ext/mbedtls

post-patch:

	@${GREP} -q '@@PREFIX@@' ${WRKSRC}/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)

	@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/libs/kfg/config.c

post-configure:

	@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP

post-build-TEST-on:	do-test

.include <bsd.port.mk>

TIMESTAMP = 1505048188

SHA256 (ncbi-ncbi-vdb-2.8.2-2_GH0.tar.gz) = 7866f7abf00e35faaa58eb3cdc14785e6d42bde515de4bb3388757eb0c8f3c95

SIZE (ncbi-ncbi-vdb-2.8.2-2_GH0.tar.gz) = 19348893

SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2

SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187

# ===========================================================================

#

#                            PUBLIC DOMAIN NOTICE

#               National Center for Biotechnology Information

#

#  This software/database is a "United States Government Work" under the

#  terms of the United States Copyright Act.  It was written as part of

#  the author's official duties as a United States Government employee and

#  thus cannot be copyrighted.  This software/database is freely available

#  to the public for use. The National Library of Medicine and the U.S.

#  Government have not placed any restriction on its use or reproduction.

#

#  Although all reasonable efforts have been taken to ensure the accuracy

#  and reliability of the software and data, the NLM and the U.S.

#  Government do not and cannot warrant the performance or results that

#  may be obtained by using this software or data. The NLM and the U.S.

#  Government disclaim all warranties, express or implied, including

#  warranties of performance, merchantability or fitness for any particular

#  purpose.

#

#  Please cite the author in any work or product based on this material.

#

# ===========================================================================

# default compiler

ifeq (,$(COMP))

	COMP = clang

endif

# handle attempts to set cross-compilation architecture

# note that if your installation is set up for cross compilation,

# you can try to enable it on your own.

ifeq (i386,$(ARCH))

i386:

	@ true

x86_64:

	@ echo "FreeBSD builds do not support cross-compilation to this architecture"

endif

ifeq (x86_64,$(ARCH))

i386:

	@ echo "FreeBSD builds do not support cross-compilation to this architecture"

x86_64:

	@ true

endif

.PHONY: i386 x86_64

# library prefix

LPFX = lib

# file extensions

OBJX = o

LOBX = pic.o

LIBX = a

SHLX = so

# compilation defines

DEFINES	:= -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS)

# FreeBSD is a Unix variant; for most cases, linux sources do well

OS_DAD = linux

OS_GDAD = unix

# flex+bison: on Mac, use source-controlled generated .c/.h files

YACC = @ true

LEX = @ true

# build matrix

COMPILERS = CLANG GCC

--- build/Makefile.clang.orig	2017-07-14 21:55:36 UTC

+++ build/Makefile.clang

@@ -22,25 +22,27 @@

 #

 # ===========================================================================

+CCNAME  ?= clang

+CXXNAME ?= clang++

 # compilers

-CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \

+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \

 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD

-CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \

+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \

 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD

 # C preprocessor

-PP = gcc -E $(CFLAGS)

+PP = $(CCNAME) -E $(CFLAGS)

 # linkers

-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \

+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \

 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \

 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \

 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

 LPFLAGS = $(LDFLAGS)

-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \

+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \

 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \

 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \

 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

--- build/Makefile.env.orig	2017-07-14 21:55:36 UTC

+++ build/Makefile.env

@@ -324,16 +324,35 @@ INCDIRS = \

 	$(addprefix -I,$(XTINC) $(NGSINC)) \

 	-I.

+# linker paths

+LDPATHS =

+

+ifneq (,$(HDF5_LIBDIR))

+	LDPATHS += -L$(HDF5_LIBDIR)

+endif

+ifneq (,$(XML2_LIBDIR))

+	LDPATHS += -L$(XML2_LIBDIR)

+endif

+ifneq (,$(MAGIC_LIBDIR))

+	LDPATHS += -L$(MAGIC_LIBDIR)

+endif

+ifneq (,$(MBEDTLS_LIBDIR))

+	LDPATHS += -L$(MBEDTLS_LIBDIR)

+endif

+ifneq (,$(FUSE_LIBDIR))

+	LDPATHS += -L$(FUSE_LIBDIR)

+endif

+

 # defines that describe os & architecture

 DLLX ?= $(SHLX)

 ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)

 # default tool parameters

-CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

-CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

+CFLAGS	= $(PKGCFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

+CPFLAGS = $(CXXFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

 # some LDFLAGS may have been specified in $(CONFIG_FILE)

-LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)

+LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)

 #-------------------------------------------------------------------------------

 # runtests

--- build/Makefile.gcc.orig	2017-07-14 21:55:36 UTC

+++ build/Makefile.gcc

@@ -22,25 +22,27 @@

 #

 # ===========================================================================

+CCNAME  ?= gcc

+CXXNAME ?= g++

 # compilers

-CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \

+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \

 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD

-CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \

+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \

 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD

 # C preprocessor

-PP = gcc -E $(CFLAGS)

+PP = $(CCNAME) -E $(CFLAGS)

 # linkers

-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \

+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \

 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \

 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \

 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

 LPFLAGS = $(LDFLAGS)

-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \

+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \

 	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \

 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \

 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)

--- build/Makefile.install.orig	2017-07-14 21:55:36 UTC

+++ build/Makefile.install

@@ -58,7 +58,7 @@ LIBRARIES_TO_INSTALL = \

     ncbi-wvdb.$(VERSION_SHLX) \

     ncbi-ngs-c++.$(VERSION_LIBX) \

-LIB_TARGET = $(INST_LIBDIR)$(BITS)

+LIB_TARGET = $(INST_LIBDIR)

 LIBRARIES_WITH_PREFIX = \

 	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))

--- build/Makefile.shell.orig	2017-07-14 21:55:36 UTC

+++ build/Makefile.shell

@@ -36,6 +36,9 @@ endif

 ifeq (Linux, $(UNAME))

 	HOST_OS = linux

 endif

+ifeq (FreeBSD, $(UNAME))

+	HOST_OS = bsd

+endif

 ifeq (SunOS, $(UNAME))

 	HOST_OS = sun

 	ARCHITECTURES = x86_64 i386

@@ -83,6 +86,9 @@ else

 	ifeq (x86_64, $(MARCH))

 		HOST_ARCH = x86_64

 	endif

+	ifeq (amd64, $(MARCH))

+		HOST_ARCH = x86_64

+	endif

 	ifeq (i86pc, $(MARCH))

 		HOST_ARCH = x86_64

 		ARCHITECTURES = x86_64 i386

@@ -93,7 +99,7 @@ else

 	endif

 endif

-ARCH = $(HOST_ARCH)

+override ARCH = $(HOST_ARCH)

 REMOTE_ARCH = $(ARCH)

 # pick up dependencies from object directory

--- build/ld.bsd.dlib.sh.orig	2017-10-27 07:23:08 UTC

+++ build/ld.bsd.dlib.sh

@@ -51,8 +51,8 @@ case "$LD" in

 g*)

     source "${0%dlib.sh}gcc.sh"

     ;;

-i*)

-    source "${0%dlib.sh}icc.sh"

+c*)

+    source "${0%dlib.sh}clang.sh"

     ;;

  *)

     echo "$SELF_NAME: unrecognized ld tool - '$LD'"

@@ -100,7 +100,7 @@ then

             # always load libdl as shared library

             load-ref-symbols

             load-dynamic

-            CMD="$CMD -ldl"

+#            CMD="$CMD -ldl"

             ;;

         -l*)

--- build/ld.bsd.exe.sh.orig	2017-10-27 07:23:08 UTC

+++ build/ld.bsd.exe.sh

@@ -51,8 +51,8 @@ case "$LD" in

 g*)

     source "${0%exe.sh}gcc.sh"

     ;;

-i*)

-    source "${0%exe.sh}icc.sh"

+c*)

+    source "${0%exe.sh}clang.sh"

     ;;

 *)

     echo "$SELF_NAME: unrecognized ld tool - '$LD'"

@@ -108,7 +108,7 @@ then

             # always load libdl as shared library

             load-ref-symbols

             load-dynamic

-            CMD="$CMD -ldl"

+#            CMD="$CMD -ldl"

             ;;

         -l*)

--- build/ld.sh.orig	2017-10-27 07:23:08 UTC

+++ build/ld.sh

@@ -68,6 +68,8 @@ HAVE_M=0

 NEED_M=1

 HAVE_XML=0

 NEED_XML=0

+HAVE_MBEDTLS=0

+NEED_MBEDTLS=0

 HAVE_KFC=0

 HAVE_KAPP=0

 HAVE_NCBI_VDB=0

@@ -297,18 +299,19 @@ do

     -[lds]ncbi-vdb)

         HAVE_NCBI_VDB=1

         KPROC=4

-        HAVE_GZIP=1

-        HAVE_BZIP=1

+        NEED_GZIP=1

+        NEED_BZIP=1

         HAVE_KFC=1

         NEED_M=1

         NEED_XML=1

+        NEED_MBEDTLS=1

         LIBS="$LIBS $1"

         ;;

     -[lds]ncbi-ngs-c++)

         HAVE_NCBI_VDB=1

         KPROC=4

-        HAVE_GZIP=1

-        HAVE_BZIP=1

+        NEED_GZIP=1

+        NEED_BZIP=1

         HAVE_KFC=1

         NEED_M=1

         NEED_XML=1

@@ -317,11 +320,12 @@ do

     -[lds]ncbi-wvdb)

         HAVE_NCBI_WVDB=1

         KPROC=4

-        HAVE_GZIP=1

-        HAVE_BZIP=1

+        NEED_GZIP=1

+        NEED_BZIP=1

         HAVE_KFC=1

         NEED_M=16

         NEED_XML=1

+        NEED_MBEDTLS=1

         LIBS="$LIBS $1"

         ;;

@@ -512,6 +516,7 @@ fi

 # supply missing libraries

 [ $HAVE_GZIP -eq 0 ] && [ $NEED_GZIP -ne 0 ] && LIBS="$LIBS -lz"

 [ $HAVE_BZIP -eq 0 ] && [ $NEED_BZIP -ne 0 ] && LIBS="$LIBS -lbz2"

+[ $HAVE_MBEDTLS -eq 0 ] && [ $NEED_MBEDTLS -ne 0 ] && LIBS="$LIBS -lmbedtls -lmbedcrypto -lmbedx509"

 [ $HAVE_DL -eq 0 ] && [ $NEED_DL -ne 0 ] && LIBS="$LIBS -ldl"

 [ $HAVE_M -eq 0 ] && [ $NEED_M -ne 0 ] && HAVE_M=16

 [ $HAVE_XML -eq 0 ] && [ $NEED_XML -ne 0 ] && HAVE_XML=32

To omit building bundled libraries.

--- libs/Makefile.orig	2017-07-14 21:55:36 UTC

+++ libs/Makefile

@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config

 # default

 #

 SUBDIRS =    \

-	ext      \

 	kfc      \

 	klib     \

 	kproc    \

--- libs/kfg/config.c.orig	2017-07-14 21:55:36 UTC

+++ libs/kfg/config.c

@@ -2558,7 +2558,7 @@ bool load_from_std_location ( KConfig *s

     const char * std_locs [] =

     {

 #if ! WINDOWS

-        "/etc/ncbi",

+        @@PREFIX@@ "/etc/ncbi",

 #else

         "/c/ncbi",

 #endif

@@ -2816,6 +2816,8 @@ void add_predefined_nodes ( KConfig * se

     #define OS "win"

 #elif SUN

     #define OS "sun"

+#elif BSD

+    #define OS "bsd"

 #else

     #error unrecognized OS

 #endif

--- libs/klib/unix/systime.c.orig	2017-07-14 21:55:36 UTC

+++ libs/klib/unix/systime.c

@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co

         t . tm_isdst = self -> dst;

         ts = mktime ( &t );

-        ts -= timezone;

+        ts += localtime(&ts)->tm_gmtoff;

     }

     return ts;

--- libs/kns/Makefile.orig	2017-07-14 21:55:36 UTC

+++ libs/kns/Makefile

@@ -39,6 +39,10 @@ OBJFILES = \

 include $(TOP)/build/Makefile.env

+ifdef MBEDTLS_INCDIR

+	INCDIRS += $(addprefix -I,$(MBEDTLS_INCDIR))

+endif

+

 RWORKDIR = $(TOP)/$(MODULE)

 #-------------------------------------------------------------------------------

--- libs/kns/unix/syssock.c.orig	2017-07-14 21:55:36 UTC

+++ libs/kns/unix/syssock.c

@@ -66,6 +66,7 @@

 #include <sys/types.h>

 #include <sys/socket.h>

 #include <sys/un.h>

+#include <netinet/in.h>

 #include <netinet/tcp.h>

 #include <poll.h>

 #include <unistd.h>

--- libs/ncbi-vdb/Makefile.orig	2017-07-14 21:55:36 UTC

+++ libs/ncbi-vdb/Makefile

@@ -87,14 +87,15 @@ LDFLAGS += -L$(XML2_LIBDIR)

 endif

 endif

+ifneq (,$(MBEDTLS_LIBDIR))

+LDFLAGS += -L$(MBEDTLS_LIBDIR)

+endif

+

 VDB_LIB_CMN =    \

 	align-access \

 	ncbi-bam     \

 	vfs          \

 	$(LIBKXML)   \

-	mbedx509     \

-	mbedtls      \

-	mbedcrypto   \

 	kns          \

 	kfg          \

 	krypto       \

@@ -103,9 +104,7 @@ VDB_LIB_CMN =    \

 	klib         \

 	kproc        \

 	$(LIBKQ)     \

-	kfc          \

-	bz2          \

-	z

+	kfc

 VDB_LIB_RD =              \

 	align-reader          \

--- libs/search/Makefile.orig	2017-07-14 21:55:36 UTC

+++ libs/search/Makefile

@@ -39,6 +39,9 @@ OBJFILES = \

 include $(TOP)/build/Makefile.env

+CARCH += -msse2

+# nucstrstr.c requires SSE2

+

 #-------------------------------------------------------------------------------

 # outer targets

 #

--- setup/konfigure.perl.orig	2017-07-14 21:55:36 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);

         $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';

@@ -762,13 +779,13 @@ 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);

@@ -832,7 +849,7 @@ 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);

@@ -867,7 +884,7 @@ 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) \\');

@@ -978,7 +995,7 @@ 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

@@ -1008,12 +1025,12 @@ 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),%$(LIBX),$@) '

@@ -1022,7 +1039,7 @@ 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                                                 \\');

@@ -1032,15 +1049,15 @@ 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) '

@@ -1059,7 +1076,7 @@ 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),%$(EXEX),$@);     \\');

@@ -1341,7 +1358,7 @@ 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) {

@@ -1483,12 +1500,12 @@ sub find_lib {

 sub check_compiler {

     my ($t, $n, $I, @l) = @_;

-    my $tool = $TOOLS;

+    my $tool = $CC;

     if ($t eq 'L') {

         print "checking for $n library... ";

     } elsif ($t eq 'O') {

-        if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) {

+        if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) {

             print "checking whether $tool accepts $n... ";

         } else {

             return;

@@ -1518,6 +1535,9 @@ sub check_compiler {

         } elsif ($n eq 'magic') {

             $library = '-lmagic';

             $log = '#include <magic.h> \n int main() { magic_open     (0); }\n'

+        } elsif ($n eq 'mbedtls') {

+            $library = '-lmbedtls';

+            $log = '#include <mbedtls/version.h> \n int main() { mbedtls_version_get_string(0); }\n'

         } elsif ($n eq 'xml2') {

             $library  = '-lxml2';

             $library .=       ' -liconv' if ($OS eq 'mac');

@@ -1554,7 +1574,7 @@ sub check_compiler {

             my $l = $l [ $i ];

             next if ( $l && ! -d $l );

             my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ')

-                                      . ($l ? "-L$l " : ' ') . "- $library";

+                                      . ($l ? "-L$l " : ' ') . "-o a.out - $library";

             $gcc .= ' 2> /dev/null' unless ($OPT{'debug'});

             open GCC, $gcc or last;

--- setup/os-arch.prl.orig	2017-07-14 21:55:36 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);

--- setup/package.prl.orig	2017-07-14 21:55:36 UTC

+++ setup/package.prl

@@ -12,6 +12,7 @@ sub PKG { ( LNG   => 'C',

 sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include'        , },

                 { name => 'hdf5' , Include => '/usr/include'        , },

                 { name => 'magic', Include => '/usr/include'        , },

+                { name => 'mbedtls', Include => '/usr/include'        , },

                 { name => 'xml2' , Include => '/usr/include/libxml2', } ) }

 sub REQ { ( { name    => 'ngs-sdk',

               aname   => 'NGS',

@@ -55,6 +56,15 @@ sub REQ { ( { name    => 'ngs-sdk',

               include => 'magic.h',

               lib     => 'libmagic.so',

             },

+            { name    => 'mbedtls',

+              option  => 'with-mbedtls-prefix',

+              origin  => 'E',

+              type    => 'LIO',

+              pkgpath => '/usr',

+              usrpath => '$HOME',

+              include => 'mbedtls/config.h',

+              lib     => 'libmbedtls.so',

+            },

             { name    => 'xml2',

               option  => 'with-xml2-prefix',

               origin  => 'E',

--- test/kapp/run-sig-core.sh.orig	2017-10-27 07:23:08 UTC

+++ test/kapp/run-sig-core.sh

@@ -29,12 +29,12 @@ BUILD_TYPE="$3"

 SIGQUIT=3

-function killFromBackground ()

+killFromBackground ()

 {

     PARENT_PID=$1

     for I in 1 2 3 4 5

     do

-        COMMAND="ps -ef|awk '\$3==${PARENT_PID} && \$8==\"${BINARY_PATH}\"  {print \$2}'"

+        COMMAND="ps awwo pid,ppid,command|awk '\$2==${PARENT_PID} && \$3==\"${BINARY_PATH}\"  {print \$1}'"

         eval PID=\`${COMMAND}\`

         if [ "$PID" = "" ]; then

             sleep 1

@@ -44,7 +44,7 @@ function killFromBackground ()

     done

     if [ "$PID" != "" ]; then

-        kill -s $SIGQUIT $PID

+        kill -s QUIT $PID

     fi

     echo $PID > killed.pid

@@ -63,6 +63,13 @@ if [ "$HOST_OS" = "mac" ]; then

    fi

    CORE_FOLDER="/core/"

+elif [ "$HOST_OS" = "bsd" ]; then

+   if [ "`ulimit -c`" = "0" ] || [ "`/sbin/sysctl -n kern.coredump`" != "1" ]; then

+       echo "Core files are disabled. Skipping core file tests"

+       exit 0

+   fi

+

+   CORE_FOLDER="./"

 elif [ "$HOST_OS" = "linux" ]; then

    if [ "`ulimit -c`" = "0" ]; then

        echo "Core files are disabled. Skipping core file tests"

@@ -92,7 +99,7 @@ wait

 BINARY_PID=`cat killed.pid`

 rm killed.pid

-CORE_FILE="${CORE_FOLDER}core.${BINARY_PID}"

+CORE_FILE="${CORE_FOLDER}${BINARY_PATH##*/}.core"

 if [ "$BUILD_TYPE" = "dbg" ]; then

    if [ -f $CORE_FILE ]; then

--- test/kfg/kfgtest.cpp.orig	2017-07-14 21:55:36 UTC

+++ test/kfg/kfgtest.cpp

@@ -443,6 +443,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture)

     CreateAndLoad(GetName(), "var=$(OS)\n");

     #if LINUX

         #define OS "linux"

+    #elif BSD

+        #define OS "bsd"    

     #elif SUN

         #define OS "sun"    

     #elif MAC 

--- test/klib/printf-test.c.orig	2017-07-14 21:55:36 UTC

+++ test/klib/printf-test.c

@@ -503,7 +503,7 @@ rc_t run ( const char *progname )

         if ( rc == 0 )

         {

             rc = make_initial_test ( field_width, precision, " ", "s", "Kurt is having a fit" );

-#if !defined(__SunOS)  &&  !defined(__sun__)

+#if !defined(__SunOS)  &&  !defined(__sun__) && !defined(__FreeBSD__)

             /* Solaris printf doesn't cope with NULLs */

             rc = make_initial_test ( field_width, precision, " ", "s", NULL );

 #endif            

run-test-proxy-with-scheme requires a web proxy server.

--- test/kns/Makefile.orig	2017-07-14 21:55:36 UTC

+++ test/kns/Makefile

@@ -25,7 +25,7 @@

 default: runtests

-runtests: run-test-proxy-with-scheme

+runtests:

 TOP ?= $(abspath ../..)

 MODULE = test/kns

@@ -39,6 +39,10 @@ TEST_TOOLS = \

 include $(TOP)/build/Makefile.env

+ifdef MBEDTLS_INCDIR

+	INCDIRS += $(addprefix -I,$(MBEDTLS_INCDIR))

+endif

+

 EXT_TOOLS = \

 	test-proxy-with-env \

 	test-proxy-with-scheme \

@@ -124,6 +128,7 @@ $(TEST_BINDIR)/test-kns: $(KNSTEST_OBJ)

 	$(LP) --exe -o $@ $^ $(KNSTEST_LIB)

 kns: test-kns

+	if [ ! -d $(HOME)/.ncbi ]; then mkdir $(HOME)/.ncbi; fi

 	$(TEST_BINDIR)/test-kns  #-l=all

 #----------------------------------------------------------------

--- test/vdb/test-dependencies.cpp.orig	2017-07-14 21:55:36 UTC

+++ test/vdb/test-dependencies.cpp

@@ -115,7 +115,7 @@ public:

 class RefseqFixture : public DepFixture {

-  #if LINUX

+  #if LINUX || BSD

     #define PATH "kfg/linux"

   #elif MAC

     #define PATH "kfg/mac"

--- test/vfs/redirect-rejected-names-cgi-http-to-https.cpp.orig	2017-07-14 21:55:36 UTC

+++ test/vfs/redirect-rejected-names-cgi-http-to-https.cpp

@@ -148,7 +148,7 @@ struct Test : protected ncbi :: NK :: Sh

 TEST_CASE(TEST) {

-#define RESOLVER_CGI_HEAD "test.ncbi.nlm.nih."

+#define RESOLVER_CGI_HEAD "www.ncbi.nlm.nih."

 #ifdef VDB_3162

 #else

NCBI-VDB is a virtualized back-end engine library for Sequencing Read Archives.

The 'front-end' API are provided by biology/ngs-sdk port.

Although the GitHub repository also contains Java and Python codes,

this port currently builds only C- and C++-based libraries.

WWW: https://github.com/ncbi/ncbi-vdb/wiki

include/ncbi-vdb/NGS.hpp

lib/libncbi-ngs-c++-static.a

lib/libncbi-ngs-c++.a

lib/libncbi-ngs-c++.a.2

lib/libncbi-ngs-c++.a.2.8.2

lib/libncbi-vdb-static.a

lib/libncbi-vdb.a

lib/libncbi-vdb.a.2

lib/libncbi-vdb.a.2.8.2

lib/libncbi-vdb.so

lib/libncbi-vdb.so.2

lib/libncbi-vdb.so.2.8.2

lib/libncbi-wvdb-static.a

lib/libncbi-wvdb.a

lib/libncbi-wvdb.a.2

lib/libncbi-wvdb.a.2.8.2

lib/libncbi-wvdb.so

lib/libncbi-wvdb.so.2

lib/libncbi-wvdb.so.2.8.2

lib/ncbi/certs.kfg

lib/ncbi/default.kfg