7 files changed, 62 insertions, 102 deletions

diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile
index efd286d1a0d4..ca7321dc39fc 100644
--- a/biology/ngs-sdk/Makefile
+++ b/biology/ngs-sdk/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	ngs
 DISTVERSION=	2.11.0
+PORTREVISION=	1
 CATEGORIES=	biology
 PKGNAMESUFFIX=	-sdk
 
@@ -14,26 +15,30 @@ BROKEN_riscv64=		fails to configure: unsupported architecture 'FreeBSD'
 NOT_FOR_ARCHS=		powerpc64
 NOT_FOR_ARCHS_REASON=	os-arch.prl needs to be taught about powerpc64
 
-USES=		gmake perl5
-GNU_CONFIGURE=	yes
+USES=		compiler:c++11-lang gmake perl5
+USE_PERL5=	build
+USE_LDCONFIG=	yes
+
 USE_GITHUB=	yes
 GH_ACCOUNT=	ncbi
-ALL_TARGET=	default
-USE_LDCONFIG=	yes
 
-CFLAGS+=	-I${WRKSRC}/ngs-sdk/ngs/unix/${ARCH}/
+HAS_CONFIGURE=	yes
+CONFIGURE_ARGS=	--prefix="${STAGEDIR}${PREFIX}" --build-prefix="${WRKSRC}/build"
+
+ALL_TARGET=	ngs-sdk
 
-post-patch:
+post-extract:
 	@cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64
 
-do-install:
-	cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}/${PREFIX}/include
-	${INSTALL_PROGRAM} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/libngs-sdk.so.${DISTVERSION} ${STAGEDIR}${PREFIX}/lib/
-	cd ${STAGEDIR}${PREFIX}/lib/ && \
-		${LN} -s libngs-sdk.so.${DISTVERSION} libngs-sdk.so.${DISTVERSION:R:R} && \
-		${LN} -s libngs-sdk.so.${DISTVERSION:R:R} libngs-sdk.so
-.for l in libngs-c++.a libngs-adapt-c++.a
-	${INSTALL_LIB} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/${l}.${PORTVERSION} ${STAGEDIR}${PREFIX}/lib/${l}
-.endfor
+do-install: # install target from the project breaks: https://github.com/ncbi/ngs/issues/34
+	# install headers
+	cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}${PREFIX}/include
+	${RM} -r ${STAGEDIR}${PREFIX}/include/ngs/win
+	# install libraries
+	cd ${WRKSRC}/build/ngs-sdk/FreeBSD/clang/amd64/rel/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/lib
+	# remove static libs built instead of shared libs, see https://github.com/ncbi/ngs/issues/33
+	cd ${STAGEDIR}${PREFIX}/lib && ${RM} libngs-c++.a* libngs-adapt-c++.a*
+	# strip
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.2.11.0
 
 .include <bsd.port.mk>
diff --git a/biology/ngs-sdk/files/patch-Makefile b/biology/ngs-sdk/files/patch-Makefile
deleted file mode 100644
index 963de357e518..000000000000
--- a/biology/ngs-sdk/files/patch-Makefile
+++ /dev/null
@@ -1,13 +0,0 @@
---- Makefile.orig	2018-06-10 19:59:04 UTC
-+++ Makefile
-@@ -27,9 +27,7 @@ default: subdirs
- 
- # the sub-directories
- SUBDIRS =    \
--	ngs-sdk \
--	ngs-java \
--	ngs-python \
-+	ngs-sdk
- 
- SUBDIRS_CLN = \
- 	$(addsuffix _cln,$(SUBDIRS))
diff --git a/biology/ngs-sdk/files/patch-configure b/biology/ngs-sdk/files/patch-configure
deleted file mode 100644
index f83ac70d996a..000000000000
--- a/biology/ngs-sdk/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	2018-06-10 19:58:29 UTC
-+++ configure
-@@ -41,7 +41,7 @@ if [ "$FILENAME" != configure -a ! -s co
-     echo configure: error: configure should be run as ./configure
- else
-     cd $CURDIR
--    for D in ngs-sdk ngs-java ngs-python
-+    for D in ngs-sdk
-     do
-       if [ -d $D ]
-           then echo "CONFIGURING $D"
diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install
new file mode 100644
index 000000000000..b9cf320d1f6d
--- /dev/null
+++ b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install
@@ -0,0 +1,11 @@
+--- ngs-sdk/Makefile.install.orig	2021-04-12 08:00:01 UTC
++++ ngs-sdk/Makefile.install
+@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \
+     ngs-c++.$(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))
diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl
deleted file mode 100644
index 640e227e429e..000000000000
--- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl
+++ /dev/null
@@ -1,13 +0,0 @@
---- ngs-sdk/setup/install.perl.orig	2018-06-10 20:03:25 UTC
-+++ ngs-sdk/setup/install.perl
-@@ -1283,8 +1283,8 @@ sub prepare {
-             '   $_{INST_JARDIR  } = "$_{PREFIX}/jar"; ' .
-             '   $_{INST_SHAREDIR} = "$_{PREFIX}/share"; ' .
-             '   $_{INCDIR       } = "$Bin/../include"; ' .
--            '   $_{LIBDIR64     } = "$Bin/../lib64"; ' .
--            '   $_{LIBDIR32     } = "$Bin/../lib32"; ';
-+            '   $_{LIBDIR64     } = "$Bin/../lib"; ' .
-+            '   $_{LIBDIR32     } = "$Bin/../lib"; ';
-         if ($HAVE{TWO_LIBS}) {
-             $code .=
-                '$_{INST_NGSLIBDIR} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";"
diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
index 5a199c8ad1dd..ef1f8a936a62 100644
--- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
+++ b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
@@ -1,26 +1,33 @@
---- ngs-sdk/setup/konfigure.perl.orig	2020-04-01 16:34:36 UTC
+--- ngs-sdk/setup/konfigure.perl.orig	2021-03-15 18:08:20 UTC
 +++ ngs-sdk/setup/konfigure.perl
-@@ -202,7 +202,7 @@ print "checking system type... " unless ($AUTORUN);
+@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN);
  my ($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 =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'FreeBSD') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
      println "configure: error: unsupported system '$OSTYPE'";
      exit 1;
  }
-@@ -221,6 +221,10 @@ if ($OS eq 'linux') {
-     println $OS_DISTRIBUTOR unless ($AUTORUN);
- }
+@@ -225,7 +225,7 @@ if ($OS eq 'linux') {
  
-+if ($MARCH eq 'amd64') {
-+    $MARCH = 'x86_64';
-+}
-+
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
- unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
-@@ -333,6 +337,16 @@ if ($OSTYPE =~ /linux/i) {
+-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
++unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) {
+     println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'";
+     exit 1;
+ }
+@@ -312,6 +312,8 @@ my $BITS;
+ 
+ if ($MARCH =~ /x86_64/i) {
+     $BITS = 64;
++} elsif ($MARCH =~ /amd64/i) {
++    $BITS = 64;
+ } elsif ($MARCH eq 'fat86') {
+     $BITS = '32_64';
+ } elsif ($MARCH =~ /i?86/i) {
+@@ -337,6 +339,25 @@ if ($OSTYPE =~ /linux/i) {
      $OSINC = 'unix';
      $TOOLS = 'gcc' unless ($TOOLS);
      $PYTHON = 'python';
@@ -33,40 +40,16 @@
 +    $EXEX = '';
 +    $OSINC = 'unix';
 +    $TOOLS = 'clang' unless ($TOOLS);
-+    $PYTHON = 'python';
++    $PYTHON = $ENV{FREEBSD_PYTHON_CMD};
++} elsif ($OSTYPE =~ /darwin/i) {
++    $LPFX = 'lib';
++    $OBJX = 'o';
++    $LOBX = 'pic.o';
++    $LIBX = 'a';
++    $SHLX = 'dylib';
++    $EXEX = '';
++    $OSINC = 'unix';
++    $TOOLS = 'clang' unless ($TOOLS);
  } elsif ($OSTYPE =~ /darwin/i) {
      $LPFX = 'lib';
      $OBJX = 'o';
-@@ -379,11 +393,11 @@ if ($TOOLS =~ /gcc$/) {
- } elsif ($TOOLS eq 'clang') {
-     $CPP  = 'clang++' unless ($CPP);
-     $CC   = 'clang -c';
--    my $versionMin = '-mmacosx-version-min=10.10';
-+    my $versionMin = '';
-     $CP   = "$CPP -c $versionMin";
-     if ($BITS ne '32_64') {
-         $ARCH_FL = '-arch i386' if ($BITS == 32);
--        $OPT = '-O3';
-+        $OPT = $ENV{'CXXFLAGS'};
-         $AR      = 'ar rc';
-         $LD      = "clang $ARCH_FL";
-         $LP      = "$CPP $versionMin $ARCH_FL";
-@@ -508,7 +522,7 @@ foreach my $href (DEPENDS()) {
-             $I = $t if (-e $t);
-         }
-         push ( @L, File::Spec->catdir($OPT{$o}, 'lib') );
--        push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
-+        #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
-     }
-     my ($i, $l) = find_lib($_, $I, @L);
-     if (defined $i || $l) {
-@@ -929,8 +943,7 @@ EndText
-     L($F, "PIC     = $PIC") if ($PIC);
-     if ($PKG{LNG} eq 'C') {
-         if ($TOOLS =~ /clang/i) {
--   L($F, 'SONAME  = -install_name ' .
--               '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
-+   L($F, 'SONAME = -Wl,-soname=$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
-    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
-    L($F, '    -flat_namespace -undefined suppress');
-         } else {
diff --git a/biology/ngs-sdk/pkg-plist b/biology/ngs-sdk/pkg-plist
index 422d5540493d..5b9c929a1a46 100644
--- a/biology/ngs-sdk/pkg-plist
+++ b/biology/ngs-sdk/pkg-plist
@@ -87,10 +87,8 @@ include/ngs/unix/arm64/atomic32.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++.a
-lib/libngs-c++.a
+lib/libngs-adapt-c++-static.a
+lib/libngs-c++-static.a
 lib/libngs-sdk.so
 lib/libngs-sdk.so.2
 lib/libngs-sdk.so.2.11.0