biology/sra-tools: Update to 3.0.6

Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master

Reported by:    portscout

biology/sra-tools/Makefile

@@ -1,109 +1,67 @@
 PORTNAME=	sra-tools
-DISTVERSION=	2.11.0
-PORTREVISION=	4
-CATEGORIES=	biology
+DISTVERSION=	3.0.6
+CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
-WWW=		https://github.com/ncbi/sra-tools/wiki
+WWW=		https://github.com/ncbi/sra-tools
 
 LICENSE=		PD LGPL21+
 LICENSE_COMB=		multi
 LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 LICENSE_DISTFILES_LGPL21+ =
 
-ONLY_FOR_ARCHS=		amd64
-ONLY_FOR_ARCHS_REASON=	NCBI-VDB requires SSE2 instructions, no 32-bit support
+# Untested on other platforms, aarch64 support was recently added upstream
+ONLY_FOR_ARCHS=		aarch64 amd64
+ONLY_FOR_ARCHS_REASON=	Upstream explicitly supports specific platforms
 
-BUILD_DEPENDS=	bash:shells/bash \
-		${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
+BUILD_DEPENDS=	bash:shells/bash
 LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
 		libhdf5.so:science/hdf5 \
-		libepoll-shim.so:devel/libepoll-shim
+		libepoll-shim.so:devel/libepoll-shim \
+		libzstd.so:archivers/zstd
 
-USES=		compiler:c11 gmake localbase:ldflags perl5 shebangfix
-USE_PERL5=	build
+USES=		bison cmake shebangfix
 USE_GITHUB=	yes
+USE_LDCONFIG=	${PREFIX}/lib64
+USE_JAVA=	yes
 
-SHEBANG_GLOB=	*.sh *.pl
+# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
+JAVA_VERSION=	17+
+
+OPTIONS_DEFINE=	EXAMPLES
+
+SHEBANG_GLOB=	*.sh
 GH_ACCOUNT=	ncbi
-GH_TUPLE+=	ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk
 GH_TUPLE+=	ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
 
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--with-ngs-sdk-prefix=${LOCALBASE} \
-		--with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \
-		--with-xml2-prefix=${LOCALBASE} \
-		--with-hdf5-prefix=${LOCALBASE} \
-		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \
-		--with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE})
-MAKE_ARGS=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
-		INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
+WITH_DEBUG=	yes
+CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
 
-NCBI_VDB_WRKSRC=	${WRKSRC}/ncbi-vdb
-NCBI_VDB_FILESDIR=	${FILESDIR}
-FREEBSD_RELEASE=	uname -r | cut -d - -f 1
-
-CFLAGS+=	-I${WRKSRC}/interfaces/os/sun
-CXXFLAGS+=	-I${WRKSRC}/interfaces/os/sun
-
-CONFLICTS_INSTALL=	kget
-
-BINARY_ALIAS=	gcc=${CC} g++=${CXX}
-
-# for port developers, building with these options may fail
-OPTIONS_DEFINE=		DEBUG OPTIMIZED_CFLAGS TEST
-DEBUG_PREVENTS=		OPTIMIZED_CFLAGS
-DEBUG_CONFIGURE_WITH=	debug
-OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
-TEST_TEST_TARGET=	test
-TEST_USES=		python
-
-# ncbi-vdb build extras
-VDB_CONFIGURE_ARGS=	\
-		--with-xml2-prefix=${LOCALBASE} \
-		--with-hdf5-prefix=${LOCALBASE} \
-		--prefix=${PREFIX} \
-		--build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
-		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
-VDB_MAKE_ARGS+=	-j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
-MAKE_ENV+=	CPATH="${LOCALBASE}/include/libepoll-shim"
-CFLAGS+=	-I${WRKSRC}/lib
-
-pre-patch:
-	@${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/
-	@${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/
-	@${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd
-	@${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \
-		${NCBI_VDB_WRKSRC}/interfaces/os/bsd/
-
-post-patch:
-	@${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
-	@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c
-	@${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64
-
-post-patch-TEST-on:
-	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile
+post-extract:
+	@${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+	@${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+	# cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb .
 
 pre-configure:
-	@${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl
-	# same as in biology/ncbi-vdb
-	@${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/
-	@${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/
-	@${MKDIR} ${WRKSRC}/interfaces/override
-	@${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override
-	@${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override
-	@cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS}
-	@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP
-	@cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS}
+	# This follows a static patch.  Run "make clean patch" before
+	# updating the patch.
+	${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \
+		${WRKSRC}/ncbi-vdb/libs/kfg/config.c
+	${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
+		${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
+	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
 
-post-build-TEST-on:	do-test
+post-stage:
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
+	${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
+	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
+	${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
+	${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
 
-do-install:
-	cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \
-	    for f in `ls *.${PORTVERSION}`; do \
-		${INSTALL_PROGRAM} $${f} \
-		${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \
-	done
+post-stage-EXAMPLES-off:
+	${RM} -r ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>

biology/sra-tools/distinfo

@@ -1,7 +1,5 @@
-TIMESTAMP = 1624382289
-SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810
-SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605
-SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc
-SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365
-SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa
-SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539
+TIMESTAMP = 1691599515
+SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348
+SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431
+SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223
+SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238

biology/sra-tools/files/Makefile.bsd

@@ -1,72 +0,0 @@
-# ===========================================================================
-#
-#                            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

biology/sra-tools/files/byteswap.h

@@ -1,40 +1,15 @@
-/*===========================================================================
-*
-*                            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.
-*
-* ===========================================================================
-*
-*/
 
-#ifndef _h_byteswap_
-#define _h_byteswap_
+#ifndef _freebsd_byteswap_h_
+#define _freebsd_byteswap_h_
 
-#include <stdint.h>
 #include <sys/endian.h>
 
-/* N.B. Sun's BSWAP seems to be macro-based,
-   meaning that (x) will be evaluated multiple times */
+#define	__BYTE_ORDER	_BYTE_ORDER
+#define	__BIG_ENDIAN	_BIG_ENDIAN
+#define	__LITTLE_ENDIAN	_LITTLE_ENDIAN
 
 #define bswap_16(x) bswap16 (x)
 #define bswap_32(x) bswap32 (x)
 #define bswap_64(x) bswap64 (x)
 
-#endif /* _h_byteswap_ */
+#endif

biology/sra-tools/files/endian.h

@@ -0,0 +1,2 @@
+
+#include <sys/endian.h>

biology/sra-tools/files/ld.bsd.clang.sh

@@ -1,47 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-# define linker params
-LD_EXPORT_GLOBAL="-Wl,--export-dynamic"
-LD_MULTIPLE_DEFS="-Wl,-zmuldefs"
-LD_STATIC="-Wl,-Bstatic"
-LD_DYNAMIC="-Wl,-Bdynamic"
-LD_ALL_SYMBOLS="-Wl,-whole-archive"
-LD_REF_SYMBOLS="-Wl,-no-whole-archive"
-
-# build command
-DLIB_CMD="$LD -shared"
-EXE_CMD="$LD"
-
-# versioned output
-if [ "$VERS" = "" ]
-then
-    DLIB_CMD="$DLIB_CMD -o $TARG"
-    EXE_CMD="$EXE_CMD -o $TARG"
-else
-    set-vers $(echo $VERS | tr '.' ' ')
-    DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-    EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
-fi

biology/sra-tools/files/ld.bsd.cmn.sh

@@ -1,158 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-# script name
-SELF_NAME="$(basename $0)"
-
-# parameters
-LD="$1"
-ARCH="$2"
-BUILD="$3"
-shift 3
-
-SRCDIR="$1"
-BINDIR="$2"
-OUTDIR="$3"
-TARG="$4"
-NAME="$5"
-DBGAP="$6"
-shift 6
-
-VERS="$1"
-VERSFILE="$2"
-DEPFILE="$3"
-shift 3
-
-MODE="$1"
-SCMFLAGS="$2"
-LDFLAGS="$3"
-shift 3
-
-LDIRS="$1"
-XDIRS="$2"
-shift 2
-
-OBJS="$1"
-LIBS="$2"
-
-# decode MODE
-STATIC=$(expr $MODE % 2)
-MODE=$(expr $MODE / 2)
-DYLD=$(expr $MODE % 2)
-MODE=$(expr $MODE / 2)
-KPROC=$(expr $MODE % 2)
-MODE=$(expr $MODE / 2)
-THREADS=$(expr $MODE % 2)
-MODE=$(expr $MODE / 2)
-HAVE_M=$(expr $MODE % 2)
-MODE=$(expr $MODE / 2)
-HAVE_XML=$(expr $MODE % 2)
-
-# decode SCMFLAGS
-CHECKSUM=$(expr $SCMFLAGS % 2)
-STATICSYSLIBS=$(expr $SCMFLAGS / 2)
-
-# return parameter for find-lib
-LIBPATH=''
-
-# initial command state
-CMD=''
-LD_STATIC_STATE=0
-LD_ALL_STATE=0
-
-# for breaking out version
-set-vers ()
-{
-    MAJ=$1
-    MIN=$2
-    REL=$3
-}
-
-# for locating libraries
-find-lib ()
-{
-    _lib="lib$1"
-    _dirs="$2"
-
-    LIBPATH=''
-
-    while [ "$_dirs" != "" ]
-    do
-        _dir="${_dirs%%:*}"
-
-        if [ "$_dir" != "" ]
-        then
-            if [ -e "$_dir/$_lib" ]
-            then
-                while [ -L "$_dir/$_lib" ]
-                do
-                    _lib=$(readlink -n "$_dir/$_lib")
-                done
-                LIBPATH="$_dir/$_lib"
-                break;
-            fi
-        fi
-
-        _dirs="${_dirs#$_dir}"
-        _dirs="${_dirs#:}"
-    done
-}
-
-# setting state
-load-static ()
-{
-    if [ $LD_STATIC_STATE -eq 0 ]
-    then
-        CMD="$CMD $LD_STATIC"
-        LD_STATIC_STATE=1
-    fi
-}
-
-load-dynamic ()
-{
-    if [ $LD_STATIC_STATE -eq 1 ]
-    then
-        CMD="$CMD $LD_DYNAMIC"
-        LD_STATIC_STATE=0
-    fi
-}
-
-load-all-symbols ()
-{
-    if [ $LD_ALL_STATE -eq 0 ]
-    then
-        CMD="$CMD $LD_ALL_SYMBOLS"
-        LD_ALL_STATE=1
-    fi
-}
-
-load-ref-symbols ()
-{
-    if [ $LD_ALL_STATE -eq 1 ]
-    then
-        CMD="$CMD $LD_REF_SYMBOLS"
-        LD_ALL_STATE=0
-    fi
-}

biology/sra-tools/files/ld.bsd.dlib.sh

@@ -1,308 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-
-# ===========================================================================
-# input library types, and their handling
-#
-#  normal linkage
-#   -l : find shared or static
-#   -s : require static
-#   -d : require shared
-#
-#  static linkage
-#   -l : require static
-#   -s : require static
-#   -d : ignore
-# ===========================================================================
-
-
-# script name
-SELF_NAME="$(basename $0)"
-BUILD_DIR="$(dirname $0)"
-
-# parameters and common functions
-source "${0%dlib.sh}cmn.sh"
-
-# discover tool chain
-case "$LD" in
-g*)
-    source "${0%dlib.sh}gcc.sh"
-    ;;
-c*)
-    source "${0%dlib.sh}clang.sh"
-    ;;
- *)
-    echo "$SELF_NAME: unrecognized ld tool - '$LD'"
-    exit 5
-esac
-
-# DLIB_CMD was started in tool-specific source
-CMD="$DLIB_CMD $LDFLAGS"
-
-# tack on object files
-CMD="$CMD $OBJS"
-
-# list of static libraries used to create dynamic lib
-SLIBS=''
-
-# initial dependency upon Makefile and vers file
-DEPS="$SRCDIR/Makefile"
-if [ "$LIBS" != "" ]
-then
-    # tack on paths
-    DIRS="$LDIRS:$XDIRS"
-    while [ "$DIRS" != "" ]
-    do
-        DIR="${DIRS%%:*}"
-        [ "$DIR" != "" ] && CMD="$CMD -L$DIR"
-        DIRS="${DIRS#$DIR}"
-        DIRS="${DIRS#:}"
-    done
-
-    # update LD_LIBRARY_PATH
-    unset LD_LIBRARY_PATH
-    export LD_LIBRARY_PATH="$LDIRS:$XDIRS"
-
-    # tack on libraries, finding as we go
-    for LIB in $LIBS
-    do
-
-        # strip off switch
-        LIBNAME="${LIB#-[lsd]}"
-
-        # look at linkage
-        case "$LIB" in
-        -ldl|-ddl)
-
-            # always load libdl as shared library
-            load-ref-symbols
-            load-dynamic
-#            CMD="$CMD -ldl"
-            ;;
-
-        -l*)
-
-            # normal or dynamic linkage
-            FOUND=0
-            if [ $STATIC -eq 0 ]
-            then
-                find-lib $LIBNAME.so $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # load normally
-                    load-ref-symbols
-                    load-dynamic
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-            fi
-
-            # try static only
-            if [ $FOUND -eq 0 ]
-            then
-                find-lib $LIBNAME.a $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # add it to dependencies
-                    DEPS="$DEPS $LIBPATH"
-                    SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                    # load static
-                    load-static
-                    load-all-symbols
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-            fi
-
-            # not found within our directories
-            if [ $FOUND -eq 0 ]
-            then
-
-                if [ $STATICSYSLIBS -eq 1 ]
-                then
-                    case "$LIBNAME" in
-                    z|bz2)
-                        # set load to static
-                        load-static
-                        load-all-symbols
-                        ;;
-
-                    *)
-                        # set load to dynamic
-                        load-ref-symbols
-                        load-dynamic
-                        ;;
-
-                    esac
-                else
-                    # set load to normal
-                    load-ref-symbols
-                    load-dynamic
-                fi
-
-                CMD="$CMD -l$LIBNAME"
-            fi
-            ;;
-
-        -s*)
-
-            # force static load
-            FOUND=0
-            find-lib $LIBNAME.a $LDIRS
-            if [ "$LIBPATH" != "" ]
-            then
-
-                # found it
-                FOUND=1
-
-                # add it to dependencies
-                DEPS="$DEPS $LIBPATH"
-                SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                # load static
-                load-static
-                load-all-symbols
-                CMD="$CMD -l$LIBNAME"
-
-            fi
-
-            # not found within our directories
-            if [ $FOUND -eq 0 ]
-            then
-
-                if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ]
-                then
-                    # set load to static
-                    load-static
-                    load-all-symbols
-                else
-
-                    case "$LIBNAME" in
-                    z|bz2)
-                        # set load to dynamic
-                        load-ref-symbols
-                        load-dynamic
-                        ;;
-
-                    *)
-                        # set load to static
-                        load-static
-                        load-all-symbols
-                        ;;
-                    esac
-                fi
-
-                CMD="$CMD -l$LIBNAME"
-            fi
-            ;;
-
-        -d*)
-
-            # only dynamic linkage
-            FOUND=0
-            if [ $STATIC -eq 0 ]
-            then
-                find-lib $LIBNAME.so $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # load normally
-                    load-ref-symbols
-                    load-dynamic
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-            fi
-
-            # not found within our directories
-            if [ $FOUND -eq 0 ]
-            then
-                # set load to normal
-                load-ref-symbols
-                load-dynamic
-                CMD="$CMD -l$LIBNAME"
-            fi
-            ;;
-
-        esac
-
-    done
-fi
-
-# put state back to normal
-load-ref-symbols
-load-dynamic
-
-# add in pthreads
-if [ $THREADS -ne 0 ]
-then
-    CMD="$CMD -lpthread"
-fi
-
-# add in xml
-if [ $HAVE_XML -ne 0 ]
-then
-    CMD="$CMD -lxml2"
-fi
-
-# add in math library
-if [ $HAVE_M -ne 0 ]
-then
-    CMD="$CMD -lm"
-fi
-
-# produce shared library
-echo "$CMD"
-$CMD || exit $?
-
-# produce dependencies
-if [ "$DEPFILE" != "" ]
-then
-    echo "$TARG: $DEPS" > "$DEPFILE"
-fi
-
-if [ $CHECKSUM -eq 1 ]
-then
-    SCM_DIR="${BUILD_DIR%/*}/scm"
-    LOGFILE="$SCM_DIR/scm.log"
-    MSG=">>>>> scm: calling the collect script from ld.linux.dlib.sh <<<<<<"
-    #echo "$MSG"
-    echo "$MSG" >> $LOGFILE
-
-    "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
-fi

biology/sra-tools/files/ld.bsd.exe.sh

@@ -1,326 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-
-# ===========================================================================
-# input library types, and their handling
-#
-#  normal linkage
-#   -l : find shared or static
-#   -s : require static
-#   -d : ignore - will be dynamically loaded
-#
-#  static linkage
-#   -l : require static
-#   -s : require static
-#   -d : require static
-# ===========================================================================
-
-
-# script name
-SELF_NAME="$(basename $0)"
-BUILD_DIR="$(dirname $0)"
-
-# parameters and common functions
-source "${0%exe.sh}cmn.sh"
-
-# discover tool chain
-case "$LD" in
-g*)
-    source "${0%exe.sh}gcc.sh"
-    ;;
-c*)
-    source "${0%exe.sh}clang.sh"
-    ;;
-*)
-    echo "$SELF_NAME: unrecognized ld tool - '$LD'"
-    exit 5
-esac
-
-# EXE_CMD was started in tool-specific source
-CMD="$EXE_CMD $LDFLAGS"
-
-# if building a static executable against dynamic libraries
-# the main application will substitute for name lookup
-if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ]
-then
-#    CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS"
-    CMD="$CMD $LD_EXPORT_GLOBAL"
-fi
-
-# tack on object files
-CMD="$CMD $OBJS"
-
-# list of static libraries used to create executable
-SLIBS=''
-
-# initial dependency upon Makefile and vers file
-DEPS="$SRCDIR/Makefile $VERSFILE"
-if [ "$LIBS" != "" ]
-then
-    # tack on paths
-    DIRS="$LDIRS:$XDIRS"
-    while [ "$DIRS" != "" ]
-    do
-        DIR="${DIRS%%:*}"
-        [ "$DIR" != "" ] && CMD="$CMD -L$DIR"
-        DIRS="${DIRS#$DIR}"
-        DIRS="${DIRS#:}"
-    done
-
-    # update LD_LIBRARY_PATH
-    unset LD_LIBRARY_PATH
-    export LD_LIBRARY_PATH="$LDIRS:$XDIRS"
-
-    # tack on libraries, finding as we go
-    for LIB in $LIBS
-    do
-
-        # strip off switch
-        LIBNAME="${LIB#-[lsd]}"
-
-        # look at linkage
-        case "$LIB" in
-        -ldl|-ddl)
-
-            # always load libdl as shared library
-            load-ref-symbols
-            load-dynamic
-#            CMD="$CMD -ldl"
-            ;;
-
-        -l*)
-
-            # normal or dynamic linkage
-            FOUND=0
-            if [ $STATIC -eq 0 ]
-            then
-                find-lib $LIBNAME.so $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # load dynamic
-                    load-dynamic
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-            fi
-
-            # try static only
-            if [ $FOUND -eq 0 ]
-            then
-                find-lib $LIBNAME.a $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # add it to dependencies
-                    DEPS="$DEPS $LIBPATH"
-                    SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                    # load static
-                    load-static
-                    [ $STATIC -eq 1 ] && load-all-symbols
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-            fi
-
-            # not found within our directories
-            if [ $FOUND -eq 0 ]
-            then
-
-                # do not need to load all symbols for external libs
-                [ $STATIC -eq 1 ] && load-ref-symbols
-
-                if [ $STATICSYSLIBS -eq 1 ]
-                then
-                    case "$LIBNAME" in
-                    z|bz2)
-                        # set load to static
-                        load-static
-                        ;;
-
-                    *)
-                        # set load to dynamic
-                        load-dynamic
-                        ;;
-
-                    esac
-                else
-                    # set load to normal
-                    load-dynamic
-                fi
-
-                CMD="$CMD -l$LIBNAME"
-            fi
-            ;;
-
-        -s*)
-
-            # force static load
-            FOUND=0
-            find-lib $LIBNAME.a $LDIRS
-            if [ "$LIBPATH" != "" ]
-            then
-
-                # found it
-                FOUND=1
-
-                # add it to dependencies
-                DEPS="$DEPS $LIBPATH"
-                SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                # load static
-                load-static
-                [ $STATIC -eq 1 ] && load-all-symbols
-                CMD="$CMD -l$LIBNAME"
-
-            fi
-
-            # not found within our directories
-            if [ $FOUND -eq 0 ]
-            then
-
-                # do not need to load all symbols for external libs
-                [ $STATIC -eq 1 ] && load-ref-symbols
-
-                if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ]
-                then
-
-                    # set load to static
-                    load-static
-
-                else
-
-                    # special case for libs we have in "ext"
-                    # that are sometimes requested as static
-                    case "$LIBNAME" in
-                    z|bz2)
-                        # set load to dynamic
-                        load-dynamic
-                        ;;
-                    *)
-                        load-static
-                        ;;
-                    esac
-                fi
-
-                CMD="$CMD -l$LIBNAME"
-            fi
-            ;;
-
-        -d*)
-
-            FOUND=0
-            if [ $STATIC -eq 1 ]
-            then
-                find-lib $LIBNAME.a $LDIRS
-                if [ "$LIBPATH" != "" ]
-                then
-
-                    # found it
-                    FOUND=1
-
-                    # add it to dependencies
-                    DEPS="$DEPS $LIBPATH"
-                    SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                    # load static
-                    load-static
-                    load-all-symbols
-
-                    CMD="$CMD -l$LIBNAME"
-
-                fi
-
-                # not found within our directories
-                if [ $FOUND -eq 0 ]
-                then
-                    load-static
-                    load-all-symbols
-
-                    CMD="$CMD -l$LIBNAME"
-                fi
-            fi
-            ;;
-
-
-        esac
-
-    done
-fi
-
-# return to normal
-load-ref-symbols
-load-dynamic
-
-# add in pthreads
-if [ $THREADS -ne 0 ]
-then
-    CMD="$CMD -lpthread"
-fi
-
-# add in xml
-# Doesn't work since ld.sh uses HAVE_XML=32, passed here as part of MODE
-if [ "$HAVE_XML2" = "1" ]
-then
-    CMD="$CMD -lxml2"
-fi
-
-# For sra-tools tools/*
-CMD="$CMD -lepoll-shim -lxml2 -lbz2 -lz"
-
-# add in math library
-if [ $HAVE_M -ne 0 ]
-then
-    CMD="$CMD -lm"
-fi
-
-# produce shared library
-echo $CMD
-$CMD || exit $?
-
-# produce dependencies
-if [ "$DEPFILE" != "" ]
-then
-    echo "$TARG: $DEPS" > "$DEPFILE"
-fi
-
-if [ $CHECKSUM -eq 1 ]
-then
-    SCM_DIR="${BUILD_DIR%/*}/scm"
-    LOGFILE="$SCM_DIR/scm.log"
-    MSG=">>>>> scm: calling the collect script from ld.linux.exe.sh <<<<<<"
-    #echo "$MSG"
-    echo "$MSG" >> $LOGFILE
-
-    "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
-fi

biology/sra-tools/files/ld.bsd.gcc.sh

@@ -1,47 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-# define linker params
-LD_EXPORT_GLOBAL="-Wl,--export-dynamic"
-LD_MULTIPLE_DEFS="-Wl,-zmuldefs"
-LD_STATIC="-Wl,-Bstatic"
-LD_DYNAMIC="-Wl,-Bdynamic"
-LD_ALL_SYMBOLS="-Wl,-whole-archive"
-LD_REF_SYMBOLS="-Wl,-no-whole-archive"
-
-# build command
-DLIB_CMD="$LD -shared"
-EXE_CMD="$LD"
-
-# versioned output
-if [ "$VERS" = "" ]
-then
-    DLIB_CMD="$DLIB_CMD -o $TARG"
-    EXE_CMD="$EXE_CMD -o $TARG"
-else
-    set-vers $(echo $VERS | tr '.' ' ')
-    DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-    EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
-fi

biology/sra-tools/files/ld.bsd.ln.sh

@@ -1,98 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-# script name
-SELF_NAME="$(basename $0)"
-
-# parameters
-TYPE="$1"
-OUTDIR="$2"
-TARG="$3"
-NAME="$4"
-DBGAP="$5"
-EXT="$6"
-VERS="$7"
-
-# find target
-TARG=$(basename "$TARG")
-
-# put extension back onto name
-NAME="$NAME$DBGAP"
-STATIC_NAME="$NAME-static"
-if [ "$EXT" != "" ]
-then
-    NAME="$NAME.$EXT"
-    STATIC_NAME="$STATIC_NAME.$EXT"
-fi
-
-# break out version
-set-vers ()
-{
-    MAJ=$1
-    MIN=$2
-    REL=$3
-}
-
-set-vers $(echo $VERS | tr '.' ' ')
-
-cd "$OUTDIR" || exit 5
-
-# create link
-create-link ()
-{
-    rm -f "$2"
-    local CMD="ln -s $1 $2"
-    echo $CMD
-    $CMD
-}
-
-# test for version in target name
-if [ "$TARG" != "$NAME.$MAJ.$MIN.$REL" ]
-then
-
-    # for simple name, create 2 links
-    if [ "$TARG" = "$NAME" ]
-    then
-        create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ"
-        create-link "$NAME.$MAJ" "$NAME"
-
-        # for static libraries, create special link
-        if [ "$TYPE" = "slib" ]
-        then
-            create-link "$NAME" "$STATIC_NAME"
-        fi
-
-    # for name with major version in it
-    elif [ "$TARG" = "$NAME.$MAJ" ]
-    then
-        create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ"
-
-
-    # for name with major & minor version in it
-    elif [ "$TARG" = "$NAME.$MAJ.$MIN" ]
-    then
-        create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ.$MIN"
-    fi
-fi

biology/sra-tools/files/ld.bsd.slib.sh

@@ -1,146 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-#                            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.
-#
-# ===========================================================================
-
-
-# ===========================================================================
-# input library types, and their handling
-#
-#  normal or static linkage
-#   -l : require static
-#   -s : require static
-#   -d : ignore
-# ===========================================================================
-
-# script name
-SELF_NAME="$(basename $0)"
-BUILD_DIR="$(dirname $0)"
-
-# parameters and common functions
-source "${0%slib.sh}cmn.sh"
-
-# initialize command
-CMD="ar -rc"
-
-# function to convert an archive into individual object files
-convert-static ()
-{
-    # list members
-    local path="$1"
-    local mbrs="$(ar -t $path)"
-
-    # unpack archive into temporary directory
-    mkdir -p ld-tmp
-    if ! cd ld-tmp
-    then
-        echo "$SELF_NAME: failed to cd to ld-tmp"
-        exit 5
-    fi
-    ar -x "$path"
-
-    # rename and add to source files list
-    local m=
-    for m in $mbrs
-    do
-        mv $m $LIBNAME-$m
-        CMD="$CMD ld-tmp/$LIBNAME-$m"
-    done
-
-    # return to prior location
-    cd - > /dev/null
-}
-
-# versioned output
-if [ "$VERS" = "" ]
-then
-    CMD="$CMD $TARG"
-else
-    set-vers $(echo $VERS | tr '.' ' ')
-    CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
-fi
-
-# tack on object files
-CMD="$CMD $OBJS"
-
-# list of static libraries used to create this lib
-SLIBS=''
-
-# initial dependency upon Makefile and vers file
-DEPS="$SRCDIR/Makefile"
-if [ "$LIBS" != "" ]
-then
-    # tack on libraries, finding as we go
-    for LIB in $LIBS
-    do
-
-        # strip off switch
-        LIBNAME="${LIB#-[lsd]}"
-
-        # look at linkage
-        case "$LIB" in
-        -s*)
-
-            # force static load
-            find-lib $LIBNAME.a $LDIRS
-            if [ "$LIBPATH" != "" ]
-            then
-
-                # add it to dependencies
-                DEPS="$DEPS $LIBPATH"
-                SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a"
-
-                # convert to individual object files
-                convert-static "$LIBPATH" || exit $?
-
-            fi
-            ;;
-
-        esac
-
-    done
-fi
-
-# produce static library
-echo $CMD
-$CMD || exit $?
-
-# remove temporaries
-rm -rf ld-tmp
-
-# produce dependencies
-if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ]
-then
-    echo "$TARG: $DEPS" > "$DEPFILE"
-fi
-
-if [ $CHECKSUM -eq 1 ]
-then
-    SCM_DIR="${BUILD_DIR%/*}/scm"
-    LOGFILE="$SCM_DIR/scm.log"
-    MSG=">>>>> scm: calling the collect script from ld.linux.slib.sh <<<<<<"
-    #echo "$MSG"
-    echo "$MSG" >> $LOGFILE
-
-    "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5"
-fi

biology/sra-tools/files/os-native.h

@@ -0,0 +1,43 @@
+/*===========================================================================
+*
+*                            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.
+*
+* ===========================================================================
+*
+*/
+
+#ifndef _h_os_native_
+#define _h_os_native_
+
+#ifndef _h_unix_native_
+#include "../unix/unix-native.h"
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _h_os_native_ */

biology/sra-tools/files/patch-CMakeLists.txt

@@ -0,0 +1,13 @@
+--- CMakeLists.txt.orig	2023-02-01 20:26:19 UTC
++++ CMakeLists.txt
+@@ -54,8 +54,8 @@ set(CMAKE_MODULE_PATH
+     "${CMAKE_CURRENT_SOURCE_DIR}/build"
+ )
+ 
+-set( VDB_BINDIR "${CMAKE_BINARY_DIR}/../ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
+-set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
++set( VDB_BINDIR "${CMAKE_BINARY_DIR}/ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
++set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
+ 
+ include(CTest)
+ enable_testing()

biology/sra-tools/files/patch-build_env.cmake

@@ -0,0 +1,56 @@
+--- build/env.cmake.orig	2023-07-10 16:23:35 UTC
++++ build/env.cmake
+@@ -69,11 +69,21 @@ if ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL  "Darwin" )
+     set(LIBPFX "lib")
+     set(SHLX "dylib")
+     set(STLX "a")
++elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL  "FreeBSD" )
++    set(OS "bsd")
++    set(LIBPFX "lib")
++    set(SHLX "so")
++    set(STLX "a")
+ elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL  "Linux" )
+     set(OS "linux")
+     set(LIBPFX "lib")
+     set(SHLX "so")
+     set(STLX "a")
++elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL  "NetBSD" )
++    set(OS "bsd")
++    set(LIBPFX "lib")
++    set(SHLX "so")
++    set(STLX "a")
+ elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL  "Windows" )
+     set(OS "windows")
+     set(LIBPFX "")
+@@ -91,6 +101,8 @@ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "aarc
+     set(ARCH "arm64")
+ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+     set(ARCH "x86_64")
++elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "amd64")
++    set(ARCH "x86_64")
+ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "AMD64")
+     set(ARCH "x86_64")
+ else()
+@@ -98,7 +110,11 @@ else()
+ endif ()
+ 
+ # create variables based entirely upon OS
+-if ( "mac" STREQUAL ${OS} )
++if ( "bsd" STREQUAL ${OS} )
++    add_compile_definitions( BSD UNIX )
++    set( LMCHECK "" )
++    set( EXE "" )
++elseif ( "mac" STREQUAL ${OS} )
+     add_compile_definitions( MAC BSD UNIX )
+     set( LMCHECK "" )
+     set( EXE "" )
+@@ -380,6 +396,9 @@ endif()
+ 
+ if ( "mac" STREQUAL ${OS} )
+     include_directories(${VDB_INTERFACES_DIR}/os/mac)
++    include_directories(${VDB_INTERFACES_DIR}/os/unix)
++elseif( "bsd" STREQUAL ${OS} )
++    include_directories(${VDB_INTERFACES_DIR}/os/bsd)
+     include_directories(${VDB_INTERFACES_DIR}/os/unix)
+ elseif( "linux" STREQUAL ${OS} )
+     include_directories(${VDB_INTERFACES_DIR}/os/linux)

biology/sra-tools/files/patch-build_ld.linux.exe.sh

@@ -1,11 +0,0 @@
---- build/ld.linux.exe.sh.orig	2021-06-20 16:32:05 UTC
-+++ build/ld.linux.exe.sh
-@@ -313,6 +313,8 @@ then
-     fi
- fi
- 
-+CMD="$CMD -lepoll-thread -lbz2 -lz"
-+
- # add in math library
- if [ $HAVE_M -ne 0 ]
- then

biology/sra-tools/files/patch-hdf5

@@ -1,30 +0,0 @@
---- ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h
-@@ -150,8 +150,13 @@ H5_DLL hid_t H5Oopen_by_idx(hid_t loc_id, const char *
-     H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id);
- H5_DLL htri_t H5Oexists_by_name(hid_t loc_id, const char *name, hid_t lapl_id);
- H5_DLL herr_t H5Oget_info(hid_t loc_id, H5O_info_t *oinfo);
-+#if H5_VERSION_GE(1,12,0)
-+H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, unsigned fields,
-+    hid_t lapl_id);
-+#else
- H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo,
-     hid_t lapl_id);
-+#endif
- H5_DLL herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name,
-     H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5O_info_t *oinfo,
-     hid_t lapl_id);
---- ncbi-vdb/libs/hdf5/hdf5dir.c.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/libs/hdf5/hdf5dir.c
-@@ -292,7 +292,11 @@ rc_t CC HDF5DirVisitUpdate ( HDF5Dir *self, bool recur
- static uint32_t HDF5DirPathTypeOnBuffer( const HDF5Dir *self, const char *buffer )
- {
-     H5O_info_t obj_info;
-+#if H5_VERSION_GE(1,12,0)
-+    herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5O_INFO_BASIC, H5P_DEFAULT );
-+#else
-     herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT );
-+#endif
-     if ( h5e >= 0 )
-     {
-         switch( obj_info.type )

biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt

@@ -0,0 +1,27 @@
+--- libs/ascp/CMakeLists.txt.orig	2023-07-10 16:23:35 UTC
++++ libs/ascp/CMakeLists.txt
+@@ -23,12 +23,17 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/connect.c )
++# FIXME: Add BSD-specific ascp-path.c
++# Aspera can be installed and run with linux compat
++set ( BSD_SRC ${UNIX_SRC} linux/ascp-path.c )
+ set ( LINUX_SRC ${UNIX_SRC} linux/ascp-path.c )
+ set ( MAC_SRC ${UNIX_SRC} mac/ascp-path.c )
+ set ( WIN_SRC win/connect.c win/ascp-path.c )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )
+@@ -49,4 +54,4 @@ GenerateStaticLibs(ascp
+ )
+ 
+ add_compile_definitions( __mod__="libs/ascp" )
+-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
+\ No newline at end of file
++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp

@@ -0,0 +1,10 @@
+--- libs/general-writer/general-writer.cpp.orig	2023-05-11 11:57:33 UTC
++++ libs/general-writer/general-writer.cpp
+@@ -39,6 +39,7 @@
+ #include <string.h>
+ 
+ #define PROGRESS_EVENT 0
++#define	UNUSED(x)	((void)(x))
+ 
+ namespace ncbi
+ {

biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang

@@ -1,30 +0,0 @@
---- ncbi-vdb/build/Makefile.clang.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/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)

biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env

@@ -1,25 +0,0 @@
---- ncbi-vdb/build/Makefile.env.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/build/Makefile.env
-@@ -333,6 +333,22 @@ 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$(MAGIC_LIBDIR)
-+endif
-+ifneq (,$(FUSE_LIBDIR))
-+	LDPATHS += -L$(FUSE_LIBDIR)
-+endif
-+ 
- 
- # defines that describe os & architecture
- DLLX ?= $(SHLX)

biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc

@@ -1,35 +0,0 @@
---- ncbi-vdb/build/Makefile.gcc.orig	2017-07-14 21:55:36 UTC
-+++ ncbi-vdb/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)

biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install

@@ -1,11 +0,0 @@
---- ncbi-vdb/build/Makefile.install.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/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))

biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell

@@ -1,31 +0,0 @@
---- ncbi-vdb/build/Makefile.shell.orig	2017-07-14 21:55:36 UTC
-+++ ncbi-vdb/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

biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake

@@ -0,0 +1,47 @@
+--- ncbi-vdb/build/env.cmake.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/build/env.cmake
+@@ -75,9 +75,15 @@ set(CMAKE_CXX_EXTENSIONS OFF)
+ if ( ${CMAKE_SYSTEM_NAME} STREQUAL  "Darwin" )
+     set(OS "mac")
+     set(SHLX "dylib")
++elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL  "FreeBSD" )
++    set(OS "bsd")
++    set(SHLX "so")
+ elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL  "Linux" )
+     set(OS "linux")
+     set(SHLX "so")
++elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL  "NetBSD" )
++    set(OS "bsd")
++    set(SHLX "so")
+ elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL  "Windows" )
+     set(OS "windows")
+ else()
+@@ -99,6 +105,8 @@ elseif ( ${_system_processor} STREQUAL "x86_64")
+     set(ARCH "x86_64")
+ elseif ( ${_system_processor} STREQUAL "AMD64")
+     set(ARCH "x86_64")
++elseif ( ${_system_processor} STREQUAL "amd64")
++    set(ARCH "x86_64")
+ else ()
+     message ( FATAL_ERROR "unknown architecture " ${_system_processor})
+ endif ()
+@@ -110,6 +118,9 @@ if ( "mac" STREQUAL ${OS} )
+     set(CMAKE_CXX_ARCHIVE_CREATE "<CMAKE_AR> Scr <TARGET> <LINK_FLAGS> <OBJECTS>")
+     set(CMAKE_C_ARCHIVE_FINISH   "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>")
+     set(CMAKE_CXX_ARCHIVE_FINISH "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>")
++elseif( "bsd" STREQUAL ${OS} )
++    add_compile_definitions( BSD UNIX )
++    set( LMCHECK "" )
+ elseif( "linux" STREQUAL ${OS} )
+     add_compile_definitions( LINUX UNIX )
+     set( LMCHECK -lmcheck )
+@@ -241,6 +252,9 @@ endif()
+ 
+ if ( "mac" STREQUAL ${OS} )
+     include_directories(interfaces/os/mac)
++    include_directories(interfaces/os/unix)
++elseif( "bsd" STREQUAL ${OS} )
++    include_directories(interfaces/os/bsd)
+     include_directories(interfaces/os/unix)
+ elseif( "linux" STREQUAL ${OS} )
+     include_directories(interfaces/os/linux)

biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h

@@ -1,85 +0,0 @@
---- ncbi-vdb/interfaces/os/sun/atomic32.h.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/interfaces/os/sun/atomic32.h
-@@ -1,3 +1,66 @@
-+#ifndef _h_atomic32_
-+#define _h_atomic32_
-+
-+#include <sys/types.h>
-+#include <machine/atomic.h>
-+
-+#ifdef __cplusplus
-+extern "C" {
-+#endif
-+
-+/*
-+ * /usr/src/sys/cddl/compat/opensolaris/sys/atomic.h
-+ * BSD license
-+ */
-+
-+#if defined(__i386__) || defined(__amd64__) || defined(__arm__)
-+/* No spurious failures from fcmpset. */
-+#define STRONG_FCMPSET
-+#endif
-+
-+static inline uint32_t
-+atomic_cas_32(volatile uint32_t *target, uint32_t cmp, uint32_t newval)
-+{
-+#ifdef STRONG_FCMPSET
-+    (void) atomic_fcmpset_32(target, &cmp, newval);
-+#else
-+    uint32_t expected = cmp;
-+
-+    do {
-+        if (atomic_fcmpset_32(target, &cmp, newval))
-+            break;
-+    } while (cmp == expected);
-+#endif
-+    return (cmp);
-+}
-+
-+static inline void  atomic_inc_32(volatile uint32_t *target)
-+{
-+    atomic_add_32(target, 1);
-+}
-+
-+static __inline uint32_t atomic_add_32_nv(volatile uint32_t *target, int32_t delta)
-+{
-+    return (atomic_fetchadd_32(target, delta) + delta);
-+}
-+
-+static __inline uint32_t atomic_inc_32_nv(volatile uint32_t *target)
-+{
-+    return (atomic_add_32_nv(target, 1));
-+}
-+
-+static __inline void
-+atomic_dec_32(volatile uint32_t *target)
-+{
-+    atomic_subtract_32(target, 1);
-+}
-+    
-+static __inline uint32_t
-+atomic_dec_32_nv(volatile uint32_t *target)
-+{
-+    return (atomic_fetchadd_32(target, -1) - 1);
-+}
-+
- /*===========================================================================
- *
- *                            PUBLIC DOMAIN NOTICE
-@@ -23,15 +86,6 @@
- * ===========================================================================
- *
- */
--
--#ifndef _h_atomic32_
--#define _h_atomic32_
--
--#include <sys/atomic.h>
--
--#ifdef __cplusplus
--extern "C" {
--#endif
- 
- #ifndef __inline__
- #define __inline__ inline

biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp

@@ -0,0 +1,11 @@
+--- ncbi-vdb/libs/align/samextract-lib.cpp.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/align/samextract-lib.cpp
+@@ -48,7 +48,7 @@
+ #include <stdlib.h>
+ #include <string.h>
+ 
+-#if LINUX
++#if BSD || LINUX
+ #include <unistd.h>
+ #define DFL_THREAD_COUNT ((int)sysconf( _SC_NPROCESSORS_ONLN ) - 1)
+ #else

biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile

@@ -1,12 +0,0 @@
---- ncbi-vdb/libs/ext/Makefile.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/libs/ext/Makefile
-@@ -32,9 +32,6 @@ include $(TOP)/build/Makefile.shell
- # default
- #
- SUBDIRS = \
--	zlib \
--	bzip2 \
--    magic \
- 	mbedtls
- 
- include $(TOP)/build/Makefile.targets

biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt

@@ -0,0 +1,19 @@
+--- ncbi-vdb/libs/kapp/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kapp/CMakeLists.txt
+@@ -23,12 +23,16 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/args-conv-os.c unix/sysmain.c )
++# Must patch hw.memsize -> hw.usermem
++set ( BSD_SRC ${UNIX_SRC} mac/ram.c )
+ set ( LINUX_SRC ${UNIX_SRC} linux/ram.c )
+ set ( MAC_SRC ${UNIX_SRC} mac/ram.c )
+ set ( WIN_SRC win/args-conv-os.c win/ram.c win/sysmain.c )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )

biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c

@@ -0,0 +1,17 @@
+--- ncbi-vdb/libs/kapp/mac/ram.c.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kapp/mac/ram.c
+@@ -46,7 +46,14 @@ rc_t KAppGetTotalRam ( uint64_t * totalRam )
+ 
+     assert ( totalRam != 0 );
+ 
++// FIXME: This file should probably be moved to bsd/ram.c
++#if defined(__APPLE__)
+     ret = sysctlbyname("hw.memsize", totalRam, &len, NULL, 0 );
++#elif defined(__FreeBSD__) || defined(__NetBSD__)
++    ret = sysctlbyname("hw.usermem", totalRam, &len, NULL, 0 );
++#else
++    #error "You need to add a sysctl for this platform."
++#endif
+     if ( ret < 0 )
+     {
+ 		int status = errno;

biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt

@@ -0,0 +1,25 @@
+--- ncbi-vdb/libs/kfc/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kfc/CMakeLists.txt
+@@ -23,12 +23,15 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/sysctx.c unix/sysrsrc.c )
++set ( BSD_SRC ${UNIX_SRC} )
+ set ( LINUX_SRC ${UNIX_SRC} )
+ set ( MAC_SRC ${UNIX_SRC} )
+ set ( WIN_SRC win/sysctx.c win/sysrsrc.c )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )
+@@ -48,4 +51,4 @@ set( SRC
+ GenerateStaticLibs( kfc "${SRC}" )
+ 
+ add_compile_definitions (__mod__="libs/kfc")
+-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
+\ No newline at end of file
++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c

@@ -1,20 +1,31 @@
---- ncbi-vdb/libs/kfg/config.c.orig	2021-03-15 18:16:43 UTC
+--- ncbi-vdb/libs/kfg/config.c.orig	2023-07-10 16:13:36 UTC
 +++ ncbi-vdb/libs/kfg/config.c
-@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi
+@@ -2574,7 +2574,7 @@ bool load_from_std_location ( KConfig *self, const KDi
      const char * std_locs [] =
      {
  #if ! WINDOWS
 -        "/etc/ncbi",
-+        @@PREFIX@@ "/etc/ncbi",
++        "/usr/local/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
+@@ -2588,7 +2588,7 @@ bool load_from_std_location ( KConfig *self, const KDi
+         NCBI_VDB_NO_ETC_NCBI_KFG[0] != '\0')
+     {
+         DBGMSG(DBG_KFG, DBG_FLAG(DBG_KFG),
+-            ("KFG: load from std. location /etc/ncbi is disabled. "
++            ("KFG: load from std. location /usr/local/etc/ncbi is disabled. "
+                 "NCBI_VDB_NO_ETC_NCBI_KFG='%s'\n", NCBI_VDB_NO_ETC_NCBI_KFG));
+         return loaded;
+     }
+@@ -2839,7 +2839,9 @@ void add_predefined_nodes ( KConfig * self, const char
+     update_node ( self, "kfg/arch/bits", buf, true );
+ 
+     /* *OS */
+-#if LINUX
++#if BSD
 +    #define OS "bsd"
- #else
-     #error unrecognized OS
- #endif
++#elif LINUX
+     #define OS "linux"
+ #elif MAC
+     #define OS "mac"

biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt

@@ -0,0 +1,35 @@
+--- ncbi-vdb/libs/kfs/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kfs/CMakeLists.txt
+@@ -23,6 +23,7 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/sysdir.c unix/sysdll.c unix/sysfile.c unix/syslockfile.c unix/sysmmap.c )
++set ( BSD_SRC ${UNIX_SRC} )
+ set ( LINUX_SRC ${UNIX_SRC} )
+ set ( MAC_SRC ${UNIX_SRC} )
+ set ( WIN_SRC win/directory-path.c win/sysdir.c win/sysdll.c win/sysfile.c win/syslockfile.c win/sysmmap.c
+@@ -30,6 +31,7 @@ set ( WIN_SRC win/directory-path.c win/sysdir.c win/sy
+ )
+ 
+ set ( UNIX_SRC_V2 unix/sysfile-v2.c )
++set ( BSD_SRC_V2 ${UNIX_SRC_V2} )
+ set ( LINUX_SRC_V2 ${UNIX_SRC_V2} )
+ set ( MAC_SRC_V2 ${UNIX_SRC_V2} )
+ set ( WIN_SRC_V2 win/sysfile-v2.c )
+@@ -37,6 +39,9 @@ set ( WIN_SRC_V2 win/sysfile-v2.c )
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+     include_directories( win )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
++    include_directories( unix )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+     include_directories( unix )
+@@ -106,4 +111,4 @@ GenerateStaticLibsWithDefs( kfs-nommap ${KFS_NOMMAP_SR
+ GenerateStaticLibs( kfs "${KFS_SRC}" )
+ 
+ add_compile_definitions (__mod__="libs/kfs")
+-include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )
+\ No newline at end of file
++include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} )

biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c

@@ -0,0 +1,11 @@
+--- ncbi-vdb/libs/kfs/unix/sysdir.c.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kfs/unix/sysdir.c
+@@ -2291,6 +2291,8 @@ rc_t KSysDirOpenDirRead_v1 ( const KSysDir_v1 * self,
+     rc_t rc;
+ 
+     rc = KSysDirMakePath_v1 ( self, rcOpening, true, full, sizeof full, path, args );
++    // FIXME: Remove this debug statement
++    // fprintf(stderr, "path = %s  full = %s\n", path, full);
+     if ( rc == 0 )
+     {
+         int t;

biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt

@@ -0,0 +1,18 @@
+--- ncbi-vdb/libs/klib/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/klib/CMakeLists.txt
+@@ -24,12 +24,15 @@
+ 
+ set ( UNIX_BASE_SRC unix/misc.c unix/syslog.c unix/systime.c unix/syswriter.c )
+ set ( UNIX_SRC ${UNIX_BASE_SRC} unix/syserrcode.c )
++set ( BSD_SRC ${UNIX_SRC} )
+ set ( LINUX_SRC ${UNIX_BASE_SRC} linux/syserrcode.c )
+ set ( MAC_SRC ${UNIX_SRC} )
+ set ( WIN_SRC win/misc.c win/sysalloc.c win/syserrcode.c win/syslog.c win/systime.c win/syswriter.c )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )

biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c

@@ -0,0 +1,20 @@
+--- ncbi-vdb/libs/klib/hashfile.c.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/klib/hashfile.c
+@@ -35,7 +35,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+-#if LINUX
++#if BSD || LINUX
+ #include <sys/mman.h>
+ #endif
+ 
+@@ -346,7 +346,7 @@ static void * map_calloc( KHashFile * self, size_t siz
+                 KLockUnlock( self->alloc_lock );
+                 return NULL;
+             }
+-#if LINUX
++#if BSD || LINUX
+             /* Not sure this helps */
+             madvise( (void *)self->alloc_base, req, MADV_RANDOM );
+ #endif

biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c

@@ -1,11 +1,16 @@
---- ncbi-vdb/libs/klib/unix/systime.c.orig	2017-07-14 21:55:36 UTC
+--- ncbi-vdb/libs/klib/unix/systime.c.orig	2023-07-10 16:13:36 UTC
 +++ ncbi-vdb/libs/klib/unix/systime.c
-@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co
+@@ -142,7 +142,13 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( const KTime *sel
          t . tm_isdst = self -> dst;
  
          ts = mktime ( &t );
--        ts -= timezone;
-+        ts += localtime(&ts)->tm_gmtoff;
++#ifdef __FreeBSD__
++	// This might be portable to all platforms
++	ts += localtime(&ts)->tm_gmtoff;
++#else
++	// extern global in sys/time.h on Linux and some other platforms
+         ts -= timezone;
++#endif
      }
  
      return ts;

biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt

@@ -0,0 +1,20 @@
+--- ncbi-vdb/libs/kns/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kns/CMakeLists.txt
+@@ -23,6 +23,7 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/sysmgr.c unix/syssock.c unix/sysstream.c )
++set ( BSD_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c )
+ set ( LINUX_SRC ${UNIX_SRC} linux/sysendpoint.c linux/syspoll.c )
+ set ( MAC_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c )
+ set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/syssock.c win/sysstream.c )
+@@ -30,6 +31,9 @@ set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/sysso
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+     include_directories( win )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
++    include_directories( unix )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+     include_directories( unix )

biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c

@@ -0,0 +1,11 @@
+--- ncbi-vdb/libs/kns/manager.c.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kns/manager.c
+@@ -58,7 +58,7 @@
+ #if HAVE_GNU_LIBC_VERSION_H
+ #include <gnu/libc-version.h>
+ #endif
+-#if LINUX
++#if BSD || LINUX
+ #include <arpa/inet.h>
+ #include <netinet/in.h>
+ #endif

biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c

@@ -1,4 +1,4 @@
---- ncbi-vdb/libs/kns/unix/syssock.c.orig	2017-07-14 21:55:36 UTC
+--- ncbi-vdb/libs/kns/unix/syssock.c.orig	2023-08-07 20:34:54 UTC
 +++ ncbi-vdb/libs/kns/unix/syssock.c
 @@ -66,6 +66,7 @@
  #include <sys/types.h>

biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt

@@ -0,0 +1,21 @@
+--- ncbi-vdb/libs/kproc/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/kproc/CMakeLists.txt
+@@ -23,6 +23,7 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/syscond.c unix/systhread.c unix/systimeout.c )
++set ( BSD_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c)
+ set ( LINUX_SRC ${UNIX_SRC} linux/sysbarrier.c linux/syslock.c linux/sysmgr.c )
+ set ( MAC_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c)
+ set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c win/systhread.c win/systimeout.c )
+@@ -30,6 +31,10 @@ set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+     include_directories( win )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
++    include_directories( bsd )
++    include_directories( unix )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+     include_directories( linux )

biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt

@@ -0,0 +1,18 @@
+--- ncbi-vdb/libs/ktst/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/ktst/CMakeLists.txt
+@@ -23,12 +23,15 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/systestenv )
++set ( BSD_SRC ${UNIX_SRC} )
+ set ( LINUX_SRC ${UNIX_SRC} )
+ set ( MAC_SRC ${UNIX_SRC} )
+ set ( WIN_SRC win/systestenv )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )

biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile

@@ -1,20 +0,0 @@
---- ncbi-vdb/libs/ncbi-vdb/Makefile.orig	2021-06-20 15:15:25 UTC
-+++ ncbi-vdb/libs/ncbi-vdb/Makefile
-@@ -138,9 +138,7 @@ VDB_LIB_CMN =    \
- 	klib         \
- 	kproc        \
- 	$(LIBKQ)     \
--	kfc          \
--	bz2          \
--	z            \
-+	kfc
- 
- VDB_LIB_RD =              \
- 	align-reader          \
-@@ -198,4 +196,4 @@ 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)/*

biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile

@@ -1,12 +0,0 @@
---- ncbi-vdb/libs/search/Makefile.orig	2017-07-14 21:55:36 UTC
-+++ ncbi-vdb/libs/search/Makefile
-@@ -39,6 +39,9 @@ OBJFILES = \
- 
- include $(TOP)/build/Makefile.env
- 
-+CARCH += -msse2
-+# nucstrstr.c requires SSE2
-+
- #-------------------------------------------------------------------------------
- # outer targets
- #

biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt

@@ -0,0 +1,25 @@
+--- ncbi-vdb/libs/vfs/CMakeLists.txt.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/libs/vfs/CMakeLists.txt
+@@ -23,12 +23,15 @@
+ # ===========================================================================
+ 
+ set ( UNIX_SRC unix/syskeyring.c unix/syspath.c )
++set ( BSD_SRC ${UNIX_SRC} )
+ set ( LINUX_SRC ${UNIX_SRC} )
+ set ( MAC_SRC ${UNIX_SRC} )
+ set ( WIN_SRC win/syskeyring.c win/syspath.c )
+ 
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+ elseif( "mac" STREQUAL ${OS} )
+@@ -54,4 +57,4 @@ set( SRC
+ GenerateStaticLibs( vfs "${SRC}" )
+ 
+ add_compile_definitions (__mod__="libs/vfs")
+-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+\ No newline at end of file
++include_directories(${CMAKE_CURRENT_SOURCE_DIR})

biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl

@@ -1,243 +0,0 @@
---- ncbi-vdb/setup/konfigure.perl.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/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;
-@@ -1706,7 +1724,7 @@ 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;

biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl

@@ -1,20 +0,0 @@
---- ncbi-vdb/setup/os-arch.prl.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/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';

biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp

@@ -1,11 +1,11 @@
---- ncbi-vdb/test/kfg/kfgtest.cpp.orig	2019-08-20 18:27:10 UTC
+--- ncbi-vdb/test/kfg/kfgtest.cpp.orig	2023-07-10 16:13:36 UTC
 +++ ncbi-vdb/test/kfg/kfgtest.cpp
-@@ -280,6 +280,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture)
+@@ -282,6 +282,8 @@ FIXTURE_TEST_CASE(predef_ARCHBITS, KfgFixture)
+ FIXTURE_TEST_CASE(predef_OS, KfgFixture)
+ {
      CreateAndLoad(GetName(), "var=$(OS)\n");
++    #if BSD
++        #define OS "bsd"
      #if LINUX
          #define OS "linux"
-+    #elif BSD
-+        #define OS "bsd"    
      #elif SUN
-         #define OS "sun"
-     #elif MAC

biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c

@@ -1,11 +1,11 @@
---- ncbi-vdb/test/klib/printf-test.c.orig	2019-08-20 18:27:10 UTC
+--- ncbi-vdb/test/klib/printf-test.c.orig	2023-07-10 16:13:36 UTC
 +++ ncbi-vdb/test/klib/printf-test.c
-@@ -503,7 +503,7 @@ rc_t run ( const char *progname )
+@@ -504,7 +504,7 @@ 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            
+ #if 0
+             /* The standard says this result is undefined, we shouldn't test for it, it is not consistent */

biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile

@@ -1,19 +0,0 @@
---- ncbi-vdb/test/kns/Makefile.orig	2021-03-15 18:16:43 UTC
-+++ ncbi-vdb/test/kns/Makefile
-@@ -25,7 +25,7 @@
- 
- default: runtests
- 
--runtests: run-tests run-test-proxy-with-scheme
-+runtests:
- 
- TOP ?= $(abspath ../..)
- MODULE = test/kns
-@@ -133,6 +133,7 @@ $(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
- 
- #----------------------------------------------------------------

biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp

@@ -1,11 +0,0 @@
---- ncbi-vdb/test/vdb/test-dependencies.cpp.orig	2019-08-20 18:27:10 UTC
-+++ ncbi-vdb/test/vdb/test-dependencies.cpp
-@@ -115,7 +115,7 @@ class EmptyFixture : public DepFixture { (public)
- 
- class RefseqFixture : public DepFixture {
- 
--  #if LINUX
-+  #if LINUX || BSD
-     #define PATH "kfg/linux"
-   #elif MAC
-     #define PATH "kfg/mac"

biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp

@@ -0,0 +1,12 @@
+--- ncbi-vdb/test/vdb/test-dependencies_dflt.cpp.orig	2023-07-10 16:13:36 UTC
++++ ncbi-vdb/test/vdb/test-dependencies_dflt.cpp
+@@ -139,6 +139,9 @@ class EmptyFixture : public DepFixture { (public)
+ 
+ class RefseqFixture : public DepFixture {
+ 
++  #if BSD
++    // FIXME: Should there be a separate kfg/freebsd?
++    #define PATH "kfg/linux"
+   #if LINUX
+     #define PATH "kfg/linux"
+   #elif MAC

biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp

@@ -1,11 +0,0 @@
---- ncbi-vdb/test/vfs/redirect-rejected-names-cgi-http-to-https.cpp.orig	2017-07-14 21:55:36 UTC
-+++ ncbi-vdb/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

biology/sra-tools/files/patch-setup_install.perl

@@ -1,13 +0,0 @@
---- setup/install.perl.orig	2021-03-15 18:25:25 UTC
-+++ 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\";"

biology/sra-tools/files/patch-setup_konfigure.perl

@@ -1,121 +0,0 @@
---- setup/konfigure.perl.orig	2021-03-15 18:25:25 UTC
-+++ setup/konfigure.perl
-@@ -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' || $OSTYPE =~ /freebsd/i) {
-     println "configure: error: unsupported system '$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_64/i || $MARCH =~ /amd64/i) {
-     $BITS = 64;
- } elsif ($MARCH eq 'fat86') {
-     $BITS = '32_64';
-@@ -337,6 +337,16 @@ if ($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';
-+    $TOOLS = 'clang' unless ($TOOLS);
-+    $PYTHON = 'python';
- } elsif ($OSTYPE =~ /darwin/i) {
-     $LPFX = 'lib';
-     $OBJX = 'o';
-@@ -512,7 +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 || $l) {
-@@ -934,7 +944,7 @@ EndText
-     if ($PKG{LNG} eq 'C') {
-         if ($TOOLS =~ /clang/i) {
-    L($F, 'SONAME  = -install_name ' .
--               '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
-+               '$(INST_LIBDIR)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
-    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
-    L($F, '    -flat_namespace -undefined suppress');
-         } else {
-@@ -1043,7 +1053,7 @@ EndText
-     L($F, '# directory rules');
-     if ($PKG{LNG} eq 'C') {
-         L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
--            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
-+            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR):');
-         T($F, 'mkdir -p $@');
-     } elsif ($PKG{LNG} eq 'JAVA') {
-         # test if we have jni header path
-@@ -1076,7 +1086,7 @@ EndText
-     if ($OS eq 'linux' || $OS eq 'mac') {
-         L($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, '  then                                                 \\');
-@@ -1087,7 +1097,7 @@ 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($F, '  else                                                 \\');
-@@ -1097,7 +1107,7 @@ EndText
-         L($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, '  then                                                 \\');
-@@ -1168,9 +1178,9 @@ EndText
- 	    print $F "    \$_{INCDIR       } = '" . expand("$Bin/.."      ) . "';\n";
- 	    if ($PKG{LNG} ne 'PYTHON') {
- 	        print $F "  \$_{BINDIR$BITS} = '" . expand($E_BINDIR      ) . "';\n";
--	        print $F "  \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR      ) . "';\n";
-+	        print $F "  \$_{LIBDIR} = '" . expand($E_LIBDIR      ) . "';\n";
- 	    } elsif ($OPT{PYTHON_LIB_PATH}) {
--	        print $F "  \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
-+	        print $F "  \$_{LIBDIR} = '$OPT{PYTHON_LIB_PATH}';\n";
- 	    }
- 	    print $F "    \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
- 	    print $F "    \$_{PREFIX       } = '$OPT{'prefix'}';\n";
-@@ -1406,7 +1416,7 @@ 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) {

biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c

@@ -1,10 +0,0 @@
---- tools/bam-loader/loader-imp.c.orig	2021-06-20 16:59:47 UTC
-+++ tools/bam-loader/loader-imp.c
-@@ -71,6 +71,7 @@
- #include <sysalloc.h>
- #include <atomic32.h>
- 
-+#include <sys/stat.h>
- #include <unistd.h>
- #include <fcntl.h>
- #include <sys/mman.h>

biology/sra-tools/files/patch-tools_copycat_Makefile

@@ -1,11 +0,0 @@
---- tools/copycat/Makefile.orig	2021-06-20 17:45:49 UTC
-+++ tools/copycat/Makefile
-@@ -92,7 +92,7 @@ COPYCAT_LIB = \
- 	-stk-version \
- 	-sncbi-vdb \
- 	-skff \
--	-smagic-static
-+	-smagic
- 
- 
- $(BINDIR)/copycat: $(COPYCAT_OBJ)

biology/sra-tools/files/patch-tools_driver-tool_Makefile

@@ -1,16 +0,0 @@
---- tools/driver-tool/Makefile.orig	2021-03-15 18:25:25 UTC
-+++ tools/driver-tool/Makefile
-@@ -97,7 +97,12 @@ SRATOOLS_OBJ = \
- SRATOOLS_LIB = \
- 	-sncbi-vdb \
- 	-sjson \
--	-lm
-+	-lepoll-shim \
-+	-lmbedtls \
-+	-lm \
-+	-lexecinfo \
-+	-lz \
-+	-lbz2
- 
- $(BINDIR)/sratools: $(SRATOOLS_OBJ) $(ILIBDIR)/libjson.$(LIBX)
- 	$(LP) --exe --vers $(SRCDIR)/../../shared/toolkit.vers -o $@ $^ $(SRATOOLS_LIB)

biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp

@@ -1,13 +0,0 @@
---- tools/driver-tool/cmdline.cpp.orig	2021-04-21 19:42:12 UTC
-+++ tools/driver-tool/cmdline.cpp
-@@ -50,6 +50,10 @@
- #define environ (*_NSGetEnviron())
- #endif
- 
-+#if defined(__FreeBSD__)
-+extern char **environ;
-+#endif
-+
- #define TRACE( lvl, ... ) /* ignore */
- 
- namespace ncbi

biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile

@@ -1,11 +0,0 @@
---- tools/driver-tool/utf8proc/Makefile.orig	2021-04-29 14:50:48 UTC
-+++ tools/driver-tool/utf8proc/Makefile
-@@ -79,7 +79,7 @@ libutf8proc.a: utf8proc.o
- 
- libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o
- 	$(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o
--	chmod a-x $@
-+	# FIX .so build so this will work: chmod a-x $@
- 
- libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH)
- 	ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@

biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp

@@ -0,0 +1,20 @@
+--- tools/external/driver-tool/file-path.posix.cpp.orig	2023-07-10 16:23:35 UTC
++++ tools/external/driver-tool/file-path.posix.cpp
+@@ -193,7 +193,16 @@ static char const *find_executable_path(char const *co
+ FilePath FilePath::fullPathToExecutable(char const *const *const argv, char const *const *const envp, char const *const *const extra)
+ {
+     char const *path;
+-#if LINUX
++// Assume sra-tools is installed by FreeBSD ports.  FreeBSD users
++// don't often install software by other means.  Default prefix
++// is /usr/local, but this can be overridden by the user building
++// the port.  The port can replace /usr/local using sed if that's the
++// case.
++#if BSD
++    char full_path[PATH_MAX];
++    snprintf(full_path, PATH_MAX, "/usr/local/bin/%s", argv[0]);
++    path = full_path;
++#elif LINUX
+     path = "/proc/self/exe";
+ #elif MAC
+     path = find_executable_path(extra, argv[0]);

biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp

@@ -0,0 +1,25 @@
+--- tools/external/driver-tool/sratools.cpp.orig	2023-07-10 16:23:35 UTC
++++ tools/external/driver-tool/sratools.cpp
+@@ -420,6 +420,7 @@ static int main(CommandLine const &argv)
+     enableLogging(argv.toolName.c_str());
+ #endif
+     LOG(7) << "executable path: " << (std::string)argv.fullPathToExe << std::endl;
++    // std::cerr << "executable path: " << (std::string)argv.fullPathToExe << std::endl;
+ 
+     config = new Config();
+     struct Defer { ~Defer() { delete config; config = nullptr; } } freeConfig;
+@@ -576,6 +577,14 @@ static int main(CommandLine const &argv)
+ }
+ 
+ } // namespace sratools
++
++#if BSD
++int main(int argc, char *argv[], char *envp[])
++{
++    auto const invocation = CommandLine(argc, argv, envp, nullptr);
++    return sratools::main(invocation);
++}
++#endif
+ 
+ #if MAC
+ int main(int argc, char *argv[], char *envp[], char *apple[])

biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt

@@ -0,0 +1,20 @@
+--- tools/external/vdb-config/tui/CMakeLists.txt.orig	2023-07-10 16:23:35 UTC
++++ tools/external/vdb-config/tui/CMakeLists.txt
+@@ -25,6 +25,7 @@
+ include_directories( ${CMAKE_CURRENT_SOURCE_DIR}/.. )
+ 
+ set ( UNIX_SRC unix/systui.c )
++set ( BSD_SRC bsd/systui.c )
+ set ( LINUX_SRC linux/systui.c )
+ set ( MAC_SRC bsd/systui.c )
+ set ( WIN_SRC win/systui.c )
+@@ -32,6 +33,9 @@ set ( WIN_SRC win/systui.c )
+ if ( "windows" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${WIN_SRC} )
+     #include_directories( win )
++elseif( "bsd" STREQUAL ${OS} )
++    set ( OS_SPECIFIC_SRC ${BSD_SRC} )
++    #include_directories( unix )
+ elseif( "linux" STREQUAL ${OS} )
+     set ( OS_SPECIFIC_SRC ${LINUX_SRC} )
+     #include_directories( unix )

biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c

@@ -1,11 +0,0 @@
---- tools/fastq-loader/spot-assembler.c.orig	2021-06-20 17:00:29 UTC
-+++ tools/fastq-loader/spot-assembler.c
-@@ -26,6 +26,8 @@
- 
- #include "spot-assembler.h"
- 
-+#include <sys/stat.h>
-+
- #include <klib/status.h>
- #include <klib/printf.h>
- 

biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c

@@ -0,0 +1,17 @@
+--- tools/loaders/fastq-loader/spot-assembler.c.orig	2023-08-08 12:26:35 UTC
++++ tools/loaders/fastq-loader/spot-assembler.c
+@@ -1,3 +1,4 @@
++
+ /*===========================================================================
+  *
+  *                            PUBLIC DOMAIN NOTICE
+@@ -25,6 +26,9 @@
+  */
+ 
+ #include "spot-assembler.h"
++
++// FIXME: Unsure if this is still necessary
++#include <sys/stat.h>
+ 
+ #include <klib/status.h>
+ #include <klib/printf.h>

biology/sra-tools/files/patch-tools_sra-sort_Makefile

@@ -1,13 +0,0 @@
---- tools/sra-sort/Makefile.orig	2021-06-20 22:24:20 UTC
-+++ tools/sra-sort/Makefile
-@@ -135,7 +135,9 @@ DBB_OBJ = \
- 	$(addsuffix .$(OBJX),$(DBB_SRC))
- 
- DBB_LIB = \
--	-lncbi-vdb \
-+	-sncbi-vdb \
- 
- $(BINDIR)/dump-blob-boundaries: $(DBB_OBJ)
-+	@echo "LD = ${LD}"
-+	@echo "DBB_LIB = ${DBB_LIB}"
- 	$(LD) --exe -o $@ $^ $(DBB_LIB)

biology/sra-tools/files/patch-tools_util_validate-names4.c

@@ -1,13 +0,0 @@
---- tools/util/validate-names4.c.orig	2021-06-20 17:53:25 UTC
-+++ tools/util/validate-names4.c
-@@ -30,8 +30,8 @@
- #include <klib/rc.h> /* RC */
- #include <vfs/path.h> /* VPath */
- 
--#include "../../../ncbi-vdb/libs/vfs/json-response.h" /* Response4Make4 */
--#include "../../../ncbi-vdb/libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/
-+#include "../libs/vfs/json-response.h" /* Response4Make4 */
-+#include "../libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/
- 
- #define RELEASE(type, obj) do { rc_t rc2 = type##Release(obj); \
-     if (rc2 && !rc) { rc = rc2; } obj = NULL; } while (false)

biology/sra-tools/pkg-descr

@@ -1,16 +1,13 @@
 SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
-
 SRAs operated by International Nucleotide Sequence Database Collaboration
 houses sequence reads and alignments generated by "next-gen" sequencers.
 SRA tools allows conversion of .sra files, which INSDC SRAs maintain,
 from/to other formats that the 'next-gen' sequenecers generate including:
-
 * csfasta/csqual (ABI SOLiD)
 * fastq (and fasta for writing)
 * hdf5 (PacBio, reading only)
 * qseq (older Illumina)
 * sam (writing only) / bam (reading only)
 * sff
-
 The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data
 and local SRA files.

biology/sra-tools/pkg-plist

@@ -1,57 +1,282 @@
 bin/abi-dump
-bin/abi-load
-bin/align-cache
+bin/abi-dump.3
+bin/abi-dump.3.0.6
 bin/align-info
-bin/bam-load
+bin/align-info.3
+bin/align-info.3.0.6
 bin/cache-mgr
-bin/ccextract
-bin/cg-load
+bin/cache-mgr.3
+bin/cache-mgr.3.0.6
 bin/check-corrupt
-bin/copycat
+bin/check-corrupt.3
+bin/check-corrupt.3.0.6
 bin/fasterq-dump
+bin/fasterq-dump-orig.3.0.6
+bin/fasterq-dump.3
+bin/fasterq-dump.3.0.6
 bin/fastq-dump
-bin/fastq-load
-bin/helicos-load
+bin/fastq-dump-orig.3.0.6
+bin/fastq-dump.3
+bin/fastq-dump.3.0.6
 bin/illumina-dump
-bin/illumina-load
-bin/kar
-bin/kar+
-bin/kar+meta
-bin/kdb-index
+bin/illumina-dump.3
+bin/illumina-dump.3.0.6
 bin/kdbmeta
-bin/kget
-bin/latf-load
-bin/make-read-filter
-bin/md5cp
+bin/kdbmeta.3
+bin/kdbmeta.3.0.6
 bin/ngs-pileup
-bin/pacbio-correct
-bin/pacbio-loadxml
+bin/ngs-pileup.3
+bin/ngs-pileup.3.0.6
 bin/prefetch
-bin/qual-recalib-stat
+bin/prefetch-orig.3.0.6
+bin/prefetch.3
+bin/prefetch.3.0.6
 bin/rcexplain
-bin/read-filter-redact
+bin/rcexplain.3
+bin/rcexplain.3.0.6
+bin/ref-variation
+bin/ref-variation.3
+bin/ref-variation.3.0.6
 bin/sam-dump
-bin/samview
-bin/schema-replace
+bin/sam-dump-orig.3.0.6
+bin/sam-dump.3
+bin/sam-dump.3.0.6
 bin/sff-dump
-bin/sff-load
+bin/sff-dump.3
+bin/sff-dump.3.0.6
+bin/sra-info
+bin/sra-info.3
+bin/sra-info.3.0.6
 bin/sra-pileup
-bin/sra-sort
-bin/sra-sort-cg
+bin/sra-pileup-orig.3.0.6
+bin/sra-pileup.3
+bin/sra-pileup.3.0.6
+bin/sra-search
+bin/sra-search.3
+bin/sra-search.3.0.6
 bin/sra-stat
+bin/sra-stat.3
+bin/sra-stat.3.0.6
 bin/srapath
+bin/srapath-orig.3.0.6
+bin/srapath.3
+bin/srapath.3.0.6
 bin/sratools
-bin/srf-load
-bin/test-read-write-cursor
+bin/sratools.3
+bin/sratools.3.0.6
 bin/test-sra
+bin/test-sra.3
+bin/test-sra.3.0.6
+bin/var-expand
+bin/var-expand.3
+bin/var-expand.3.0.6
 bin/vdb-config
-bin/vdb-copy
+bin/vdb-config.3
+bin/vdb-config.3.0.6
 bin/vdb-decrypt
-bin/vdb-diff
+bin/vdb-decrypt.3
+bin/vdb-decrypt.3.0.6
 bin/vdb-dump
+bin/vdb-dump-orig.3.0.6
+bin/vdb-dump.3
+bin/vdb-dump.3.0.6
 bin/vdb-encrypt
-bin/vdb-lock
-bin/vdb-passwd
-bin/vdb-sql
-bin/vdb-unlock
+bin/vdb-encrypt.3
+bin/vdb-encrypt.3.0.6
 bin/vdb-validate
+bin/vdb-validate.3
+bin/vdb-validate.3.0.6
+include/ncbi-vdb/NGS.hpp
+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/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
+jar/ngs-doc.jar
+jar/ngs-examples.jar
+jar/ngs-java.jar
+jar/ngs-src.jar
+lib64/libncbi-ngs-c++-static.a
+lib64/libncbi-ngs-c++.a
+lib64/libncbi-ngs-c++.a.3
+lib64/libncbi-ngs-c++.a.3.0.6
+lib64/libncbi-ngs-static.a
+lib64/libncbi-ngs.a
+lib64/libncbi-ngs.a.3
+lib64/libncbi-ngs.a.3.0.6
+lib64/libncbi-ngs.so
+lib64/libncbi-ngs.so.3
+lib64/libncbi-ngs.so.3.0.6
+lib64/libngs-c++-static.a
+lib64/libngs-c++.a
+lib64/libngs-c++.a.3
+lib64/libngs-c++.a.3.0.6
+lib64/libngs-c++.so
+lib64/libngs-c++.so.3
+lib64/libngs-c++.so.3.0.6
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/expected.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignSliceTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/DumpReferenceFASTA.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/FragTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/PileupTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/ReadGroupTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/RefTest.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/expected.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignSliceTest.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignTest.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/FragTest.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/PileupTest.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/RefTest.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/expected.txt
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+%%JAVASHAREDIR%%doc/ngs-doc/allpackages-index.html
+%%JAVASHAREDIR%%doc/ngs-doc/constant-values.html
+%%JAVASHAREDIR%%doc/ngs-doc/element-list
+%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
+%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
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+%%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
+%%JAVASHAREDIR%%doc/ngs-doc/help-doc.html
+%%JAVASHAREDIR%%doc/ngs-doc/index-all.html
+%%JAVASHAREDIR%%doc/ngs-doc/index.html
+%%JAVASHAREDIR%%doc/ngs-doc/jquery-ui.overrides.css
+%%JAVASHAREDIR%%doc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
+%%JAVASHAREDIR%%doc/ngs-doc/legal/ASSEMBLY_EXCEPTION
+%%JAVASHAREDIR%%doc/ngs-doc/legal/LICENSE
+%%JAVASHAREDIR%%doc/ngs-doc/legal/jquery.md
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