git: d55fba431adf - main - New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequence Read Archive
Yuri Victorovich
yuri at FreeBSD.org
Mon Apr 12 09:29:44 UTC 2021
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=d55fba431adf6bc61c3553dd91625a4b16115cf6
commit d55fba431adf6bc61c3553dd91625a4b16115cf6
Author: Yuri Victorovich <yuri at FreeBSD.org>
AuthorDate: 2021-04-12 09:29:15 +0000
Commit: Yuri Victorovich <yuri at FreeBSD.org>
CommitDate: 2021-04-12 09:29:42 +0000
New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequence Read Archive
PR: 223273
Submitted by: Motomichi Matsuzaki <mzaki at niid.go.jp> (original version)
---
biology/Makefile | 1 +
biology/ncbi-vdb/Makefile | 64 ++++++
biology/ncbi-vdb/distinfo | 5 +
biology/ncbi-vdb/files/Makefile.bsd | 72 ++++++
biology/ncbi-vdb/files/patch-build_Makefile.clang | 30 +++
biology/ncbi-vdb/files/patch-build_Makefile.env | 28 +++
biology/ncbi-vdb/files/patch-build_Makefile.gcc | 35 +++
.../ncbi-vdb/files/patch-build_Makefile.install | 11 +
biology/ncbi-vdb/files/patch-build_Makefile.shell | 31 +++
biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh | 22 ++
biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh | 22 ++
biology/ncbi-vdb/files/patch-build_ld.sh | 49 ++++
biology/ncbi-vdb/files/patch-libs_Makefile | 12 +
biology/ncbi-vdb/files/patch-libs_kfg_config.c | 20 ++
.../ncbi-vdb/files/patch-libs_klib_unix_systime.c | 11 +
biology/ncbi-vdb/files/patch-libs_kns_Makefile | 13 ++
.../ncbi-vdb/files/patch-libs_kns_linux_syspoll.c | 11 +
.../ncbi-vdb/files/patch-libs_kns_unix_syssock.c | 10 +
.../ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile | 40 ++++
biology/ncbi-vdb/files/patch-libs_search_Makefile | 12 +
biology/ncbi-vdb/files/patch-setup_konfigure.perl | 253 +++++++++++++++++++++
biology/ncbi-vdb/files/patch-setup_os-arch.prl | 20 ++
biology/ncbi-vdb/files/patch-setup_package.prl | 26 +++
.../ncbi-vdb/files/patch-test_kapp_run-sig-core.sh | 49 ++++
biology/ncbi-vdb/files/patch-test_kfg_kfgtest.cpp | 11 +
.../ncbi-vdb/files/patch-test_klib_printf-test.c | 11 +
biology/ncbi-vdb/files/patch-test_kns_Makefile | 32 +++
.../files/patch-test_vdb_test-dependencies.cpp | 11 +
...s_redirect-rejected-names-cgi-http-to-https.cpp | 11 +
biology/ncbi-vdb/pkg-descr | 7 +
biology/ncbi-vdb/pkg-plist | 17 ++
31 files changed, 947 insertions(+)
diff --git a/biology/Makefile b/biology/Makefile
index bc59c19d8905..73af8b5788bd 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -84,6 +84,7 @@
SUBDIR += ncbi-blast+
SUBDIR += ncbi-cxx-toolkit
SUBDIR += ncbi-toolkit
+ SUBDIR += ncbi-vdb
SUBDIR += ngs-sdk
SUBDIR += p5-AcePerl
SUBDIR += p5-Bio-ASN1-EntrezGene
diff --git a/biology/ncbi-vdb/Makefile b/biology/ncbi-vdb/Makefile
new file mode 100644
index 000000000000..e3ec6af6a55b
--- /dev/null
+++ b/biology/ncbi-vdb/Makefile
@@ -0,0 +1,64 @@
+PORTNAME= ncbi-vdb
+DISTVERSION= 2.11.0
+CATEGORIES= biology
+
+MAINTAINER= mzaki at niid.go.jp
+COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive
+
+LICENSE= PD
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+ONLY_FOR_ARCHS= amd64 i386
+ONLY_FOR_ARCHS_REASON= libs/search/nucstrstr.c requires SSE2 instructions
+
+BUILD_DEPENDS= bash:shells/bash \
+ libepoll-shim>0:devel/libepoll-shim
+
+LIB_DEPENDS= libxml2.so:textproc/libxml2 \
+ libhdf5.so:science/hdf5 \
+ libmbedtls.so:security/mbedtls
+
+USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix
+USE_PERL5= build
+USE_LDCONFIG= yes
+
+USE_GITHUB= yes
+GH_ACCOUNT= ncbi
+GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs # ported as biology/ngs-sdk
+
+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="${CFLAGS}"
+
+CFLAGS+= -I${WRKSRC}/lib
+
+MAKE_JOBS_UNSAFE= yes
+
+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 ${WRKSRC}/interfaces/os/bsd/
+
+post-patch:
+ @${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-install:
+ # remove static libs built instead of shared libs, see https://github.com/ncbi/ncbi-vdb/issues/36
+ cd ${STAGEDIR}${PREFIX}/lib && ${RM} libkdf5.a* libncbi-ngs-c++.a* libncbi-ngs.a* libncbi-vdb.a* libncbi-wvdb.a*
+
+.include <bsd.port.mk>
diff --git a/biology/ncbi-vdb/distinfo b/biology/ncbi-vdb/distinfo
new file mode 100644
index 000000000000..d5c8684089f1
--- /dev/null
+++ b/biology/ncbi-vdb/distinfo
@@ -0,0 +1,5 @@
+TIMESTAMP = 1618218620
+SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa
+SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539
+SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc
+SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365
diff --git a/biology/ncbi-vdb/files/Makefile.bsd b/biology/ncbi-vdb/files/Makefile.bsd
new file mode 100644
index 000000000000..7692ec277948
--- /dev/null
+++ b/biology/ncbi-vdb/files/Makefile.bsd
@@ -0,0 +1,72 @@
+# ===========================================================================
+#
+# 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
diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.clang b/biology/ncbi-vdb/files/patch-build_Makefile.clang
new file mode 100644
index 000000000000..fb43d0f3964d
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_Makefile.clang
@@ -0,0 +1,30 @@
+--- build/Makefile.clang.orig 2021-03-15 18:16:43 UTC
++++ build/Makefile.clang
+@@ -24,23 +24,23 @@
+
+
+ # 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 $(OBJX) -stdlib=libc++ --cflags "$(CPFLAGS)" -MD
+
+ # C preprocessor
+ PP = gcc -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)
diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.env b/biology/ncbi-vdb/files/patch-build_Makefile.env
new file mode 100644
index 000000000000..b6f7158d65d3
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_Makefile.env
@@ -0,0 +1,28 @@
+--- build/Makefile.env.orig 2021-03-15 18:16:43 UTC
++++ build/Makefile.env
+@@ -333,6 +333,25 @@ 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)
diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.gcc b/biology/ncbi-vdb/files/patch-build_Makefile.gcc
new file mode 100644
index 000000000000..b7df82ef7c9f
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_Makefile.gcc
@@ -0,0 +1,35 @@
+--- 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):$(ILIBDIR)
diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.install b/biology/ncbi-vdb/files/patch-build_Makefile.install
new file mode 100644
index 000000000000..edd0682cdf14
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_Makefile.install
@@ -0,0 +1,11 @@
+--- build/Makefile.install.orig 2021-03-15 18:16:43 UTC
++++ build/Makefile.install
+@@ -69,7 +69,7 @@ ifeq (1,$(HAVE_HDF5))
+ endif
+
+
+-LIB_TARGET = $(INST_LIBDIR)$(BITS)
++LIB_TARGET = $(INST_LIBDIR)
+
+ LIBRARIES_WITH_PREFIX = \
+ $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.shell b/biology/ncbi-vdb/files/patch-build_Makefile.shell
new file mode 100644
index 000000000000..c331ad799a68
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_Makefile.shell
@@ -0,0 +1,31 @@
+--- 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 = $(ARCH)
+
+ # pick up dependencies from object directory
diff --git a/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh b/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh
new file mode 100644
index 000000000000..074f7721b564
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh
@@ -0,0 +1,22 @@
+--- build/ld.bsd.dlib.sh.orig 2017-10-27 07:23:08 UTC
++++ build/ld.bsd.dlib.sh
+@@ -51,8 +51,8 @@ case "$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="$CMD -ldl"
+ ;;
+
+ -l*)
diff --git a/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh b/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh
new file mode 100644
index 000000000000..a4ea00c176f1
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh
@@ -0,0 +1,22 @@
+--- build/ld.bsd.exe.sh.orig 2017-10-27 07:23:08 UTC
++++ build/ld.bsd.exe.sh
+@@ -51,8 +51,8 @@ case "$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="$CMD -ldl"
+ ;;
+
+ -l*)
diff --git a/biology/ncbi-vdb/files/patch-build_ld.sh b/biology/ncbi-vdb/files/patch-build_ld.sh
new file mode 100644
index 000000000000..900d7e566356
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-build_ld.sh
@@ -0,0 +1,49 @@
+--- build/ld.sh.orig 2021-04-12 06:10:01 UTC
++++ build/ld.sh
+@@ -68,6 +68,8 @@ HAVE_M=0
+ NEED_M=1
+ HAVE_XML=0
+ NEED_XML=0
++HAVE_MBEDTLS=0
++NEED_MBEDTLS=0
+ HAVE_KFC=0
+ HAVE_KAPP=0
+ HAVE_NCBI_VDB=0
+@@ -297,11 +299,12 @@ do
+ -[lds]ncbi-vdb)
+ HAVE_NCBI_VDB=1
+ KPROC=4
+- HAVE_GZIP=1
+- HAVE_BZIP=1
++ NEED_GZIP=1
++ NEED_BZIP=1
+ HAVE_KFC=1
+ NEED_M=1
+ NEED_XML=1
++ NEED_MBEDTLS=1
+ LIBS="$LIBS $1"
+ ;;
+ -[lds]ncbi-ngs-c++)
+@@ -310,11 +313,12 @@ do
+ -[lds]ncbi-wvdb)
+ HAVE_NCBI_WVDB=1
+ KPROC=4
+- HAVE_GZIP=1
+- HAVE_BZIP=1
++ NEED_GZIP=1
++ NEED_BZIP=1
+ HAVE_KFC=1
+ NEED_M=16
+ NEED_XML=1
++ NEED_MBEDTLS=1
+ LIBS="$LIBS $1"
+ ;;
+
+@@ -505,6 +509,7 @@ 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
diff --git a/biology/ncbi-vdb/files/patch-libs_Makefile b/biology/ncbi-vdb/files/patch-libs_Makefile
new file mode 100644
index 000000000000..f444241b68f9
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_Makefile
@@ -0,0 +1,12 @@
+To omit building bundled libraries.
+
+--- libs/Makefile.orig 2021-03-15 18:16:43 UTC
++++ libs/Makefile
+@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config
+ # default
+ #
+ MAIN_SUBDIRS = \
+- ext \
+ kfc \
+ klib \
+ kproc \
diff --git a/biology/ncbi-vdb/files/patch-libs_kfg_config.c b/biology/ncbi-vdb/files/patch-libs_kfg_config.c
new file mode 100644
index 000000000000..d82d3e9143ed
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_kfg_config.c
@@ -0,0 +1,20 @@
+--- libs/kfg/config.c.orig 2021-03-15 18:16:43 UTC
++++ libs/kfg/config.c
+@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi
+ const char * std_locs [] =
+ {
+ #if ! WINDOWS
+- "/etc/ncbi",
++ @@PREFIX@@ "/etc/ncbi",
+ #else
+ "/c/ncbi",
+ #endif
+@@ -2850,6 +2850,8 @@ void add_predefined_nodes ( KConfig * self, const char
+ #define OS "win"
+ #elif SUN
+ #define OS "sun"
++#elif BSD
++ #define OS "bsd"
+ #else
+ #error unrecognized OS
+ #endif
diff --git a/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c b/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c
new file mode 100644
index 000000000000..781fd4b75403
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c
@@ -0,0 +1,11 @@
+--- 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;
diff --git a/biology/ncbi-vdb/files/patch-libs_kns_Makefile b/biology/ncbi-vdb/files/patch-libs_kns_Makefile
new file mode 100644
index 000000000000..6438e3f6bfa6
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_kns_Makefile
@@ -0,0 +1,13 @@
+--- 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)
+
+ #-------------------------------------------------------------------------------
diff --git a/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c b/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c
new file mode 100644
index 000000000000..4ed159f5e812
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c
@@ -0,0 +1,11 @@
+--- libs/kns/linux/syspoll.c.orig 2021-04-12 05:19:32 UTC
++++ libs/kns/linux/syspoll.c
+@@ -43,7 +43,7 @@
+ #include <unistd.h>
+ #include <errno.h>
+
+-#include <sys/epoll.h>
++#include <libepoll-shim/sys/epoll.h>
+ #include <sys/types.h>
+ #include <sys/socket.h>
+
diff --git a/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c b/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c
new file mode 100644
index 000000000000..a188b1c12539
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c
@@ -0,0 +1,10 @@
+--- 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>
diff --git a/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile b/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile
new file mode 100644
index 000000000000..724f06235fcd
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile
@@ -0,0 +1,40 @@
+--- libs/ncbi-vdb/Makefile.orig 2021-03-15 18:16:43 UTC
++++ libs/ncbi-vdb/Makefile
+@@ -121,15 +121,16 @@ LDFLAGS += -L$(XML2_LIBDIR)
+ endif
+ endif
+
++ifneq (,$(MBEDTLS_LIBDIR))
++LDFLAGS += -L$(MBEDTLS_LIBDIR)
++endif
++
+ VDB_LIB_CMN = \
+ align-access \
+ ncbi-bam \
+ vfs \
+ cloud \
+ $(LIBKXML) \
+- mbedx509 \
+- mbedtls \
+- mbedcrypto \
+ kns \
+ kfg \
+ krypto \
+@@ -138,9 +139,7 @@ VDB_LIB_CMN = \
+ klib \
+ kproc \
+ $(LIBKQ) \
+- kfc \
+- bz2 \
+- z \
++ kfc
+
+ VDB_LIB_RD = \
+ align-reader \
+@@ -198,4 +197,4 @@ fuzz:
+ $(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB)
+
+ cleanfuzz:
+- rm -rf $(FLIBDIR)/*
+\ No newline at end of file
++ rm -rf $(FLIBDIR)/*
diff --git a/biology/ncbi-vdb/files/patch-libs_search_Makefile b/biology/ncbi-vdb/files/patch-libs_search_Makefile
new file mode 100644
index 000000000000..3c01af3268be
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-libs_search_Makefile
@@ -0,0 +1,12 @@
+--- libs/search/Makefile.orig 2017-07-14 21:55:36 UTC
++++ libs/search/Makefile
+@@ -39,6 +39,9 @@ OBJFILES = \
+
+ include $(TOP)/build/Makefile.env
+
++CARCH += -msse2
++# nucstrstr.c requires SSE2
++
+ #-------------------------------------------------------------------------------
+ # outer targets
+ #
diff --git a/biology/ncbi-vdb/files/patch-setup_konfigure.perl b/biology/ncbi-vdb/files/patch-setup_konfigure.perl
new file mode 100644
index 000000000000..39a2926d5511
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-setup_konfigure.perl
@@ -0,0 +1,253 @@
+--- setup/konfigure.perl.orig 2021-03-15 18:16:43 UTC
++++ setup/konfigure.perl
+@@ -192,7 +192,7 @@ if ($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 $PACKAGE_NAME package";
+@@ -204,7 +204,7 @@ print "checking system type... " unless ($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 =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
+ println "configure: error: unsupported system '$OSTYPE'";
+ exit 1;
+ }
+@@ -225,7 +225,7 @@ if ($OS eq 'linux') {
+
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+-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;
+ }
+@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless
+
+ my $BITS;
+
+-if ($MARCH =~ /x86_64/i) {
++if ($MARCH =~ /(x86_|amd)64/i) {
+ $BITS = 64;
+ } elsif ($MARCH eq 'fat86') {
+ $BITS = '32_64';
+@@ -337,6 +337,19 @@ if ($OSTYPE =~ /linux/i) {
+ $OSINC = 'unix';
+ $TOOLS = 'gcc' unless ($TOOLS);
+ $PYTHON = 'python';
++} elsif ($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});
++ }
++ $PYTHON = $ENV{FREEBSD_PYTHON_CMD};
+ } elsif ($OSTYPE =~ /darwin/i) {
+ $LPFX = 'lib';
+ $OBJX = 'o';
+@@ -362,17 +375,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $MD, $LDFLAGS) =
+
+ print "checking for supported tool chain... " unless ($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;
+
+ $DBG = '-g -DDEBUG';
+@@ -382,21 +397,24 @@ if ($TOOLS =~ /gcc$/) {
+ $MD = '-MD';
+ } elsif ($TOOLS eq 'clang') {
+ $CPP = 'clang++' unless ($CPP);
+- $CC = 'clang -c';
+- my $versionMin = '-mmacosx-version-min=10.10';
++ $CC = 'clang' unless ($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";
+ }
+ $ARX = 'ar x';
+@@ -826,13 +844,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os-arch.perl)
+ # install paths
+ EndText
+
+- L($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);
+@@ -896,7 +914,7 @@ 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 $MARCH);
+@@ -932,7 +950,7 @@ EndText
+ }
+ L($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 $(VERSION) \\');
+@@ -1043,7 +1061,7 @@ EndText
+ L($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
+@@ -1073,12 +1091,12 @@ 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),%$(LIBX),$@) '
+@@ -1087,7 +1105,7 @@ 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($F, ' else \\');
+@@ -1097,15 +1115,15 @@ EndText
+ L($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 $(@F) '
+@@ -1124,7 +1142,7 @@ EndText
+
+ L($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),%$(EXEX),$@); \\');
+@@ -1406,7 +1424,7 @@ 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 $f) {
+@@ -1628,12 +1646,12 @@ sub find_lib {
+
+ sub check_compiler {
+ my ($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 $n... ";
+ } else {
+ return;
+@@ -1663,6 +1681,9 @@ sub check_compiler {
+ } elsif ($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');
+@@ -1706,7 +1727,7 @@ sub check_compiler {
+ }
+ }
+ 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;
diff --git a/biology/ncbi-vdb/files/patch-setup_os-arch.prl b/biology/ncbi-vdb/files/patch-setup_os-arch.prl
new file mode 100644
index 000000000000..28d9b469c744
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-setup_os-arch.prl
@@ -0,0 +1,20 @@
+--- setup/os-arch.prl.orig 2021-03-15 18:16:43 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/) {
+@@ -48,6 +50,8 @@ sub OsArch {
+ $HOST_ARCH = 'i386';
+ }
+ } elsif ($MARCH =~ /x86_64/) {
++ $HOST_ARCH = 'x86_64';
++ } elsif ($MARCH =~ /amd64/) {
+ $HOST_ARCH = 'x86_64';
+ } elsif ($MARCH =~ /i86pc/) {
+ $HOST_ARCH = 'x86_64';
diff --git a/biology/ncbi-vdb/files/patch-setup_package.prl b/biology/ncbi-vdb/files/patch-setup_package.prl
new file mode 100644
index 000000000000..7f44d3a7e79d
--- /dev/null
+++ b/biology/ncbi-vdb/files/patch-setup_package.prl
@@ -0,0 +1,26 @@
+--- setup/package.prl.orig 2021-03-15 18:16:43 UTC
++++ setup/package.prl
+@@ -12,6 +12,7 @@ sub PKG { ( LNG => 'C',
+ sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include' , },
+ { name => 'hdf5' , Include => '/usr/include' , },
+ { name => 'magic', Include => '/usr/include' , },
++ { name => 'mbedtls', Include => '/usr/include' , },
+ { name => 'xml2' , Include => '/usr/include/libxml2', } ) }
+ sub REQ { ( { name => 'ngs-sdk',
+ aname => 'NGS',
+@@ -54,6 +55,15 @@ sub REQ { ( { name => 'ngs-sdk',
+ usrpath => '$HOME',
+ 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',
+ },
*** 199 LINES SKIPPED ***
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