biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives

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. This port is a bit convoluted due to the fact that the sra-tools build requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated as a submodule here rather than a separate library port. We are working with upstream with hope for long-term improvements.
author: Jason W. Bacon <jwb@FreeBSD.org> 2021-06-22 17:55:15 +0000
committer: Jason W. Bacon <jwb@FreeBSD.org> 2021-06-22 17:55:15 +0000
commit: 69656bf0d7d99660e536c22472a5eae639695a97 (patch)
tree: 1eec14b05b8f280276d6e0dbc1063d9f91d4a327 /biology
parent: 754ca6f4c9c3c1ce86e13bdf62db3e3282346cbf (diff)
download: ports-69656bf0d7d99660e536c22472a5eae639695a97.tar.gz
ports-69656bf0d7d99660e536c22472a5eae639695a97.zip
45 files changed, 2350 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile
index ec9728ced8ee..158eb70ede1a 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -175,6 +175,7 @@
     SUBDIR += smithwaterman
     SUBDIR += snpeff
     SUBDIR += spoa
+    SUBDIR += sra-tools
     SUBDIR += stacks
     SUBDIR += star
     SUBDIR += stringtie
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
new file mode 100644
index 000000000000..0b6a54bd67ca
--- /dev/null
+++ b/biology/sra-tools/Makefile
@@ -0,0 +1,105 @@
+PORTNAME=	sra-tools
+DISTVERSION=	2.11.0
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
+
+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
+
+BUILD_DEPENDS=	bash:shells/bash \
+		${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
+LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
+		libhdf5.so:science/hdf5 \
+		libepoll-shim.so:devel/libepoll-shim
+
+USES=		compiler:c11 gmake localbase:ldflags perl5 shebangfix
+USE_PERL5=	build
+USE_GITHUB=	yes
+
+SHEBANG_GLOB=	*.sh *.pl
+GH_ACCOUNT=	ncbi
+GH_TUPLE+=	ncbi:ngs:${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$$(${FREEBSD_RELEASE})
+MAKE_ARGS=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
+		INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
+
+NCBI_VDB_WRKSRC=	${WRKSRC}/ncbi-vdb
+NCBI_VDB_FILESDIR=	${FILESDIR}
+FREEBSD_RELEASE=	uname -r | cut -d - -f 1
+
+CFLAGS+=	-I${WRKSRC}/interfaces/os/sun
+CXXFLAGS+=	-I${WRKSRC}/interfaces/os/sun
+
+BINARY_ALIAS=	gcc=${CC} g++=${CXX}
+
+# for port developers, building with these options may fail
+OPTIONS_DEFINE=		DEBUG OPTIMIZED_CFLAGS TEST
+DEBUG_PREVENTS=		OPTIMIZED_CFLAGS
+DEBUG_CONFIGURE_WITH=	debug
+OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
+TEST_TEST_TARGET=	test
+TEST_USES=		python
+
+# ncbi-vdb build extras
+VDB_CONFIGURE_ARGS=	\
+		--with-xml2-prefix=${LOCALBASE} \
+		--with-hdf5-prefix=${LOCALBASE} \
+		--prefix=${PREFIX} \
+		--build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
+		CC="${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}|' ${WRKSRC}/test/kget/Makefile
+
+pre-configure:
+	@${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}
+
+post-build-TEST-on:	do-test
+
+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
+
+.include <bsd.port.mk>
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
new file mode 100644
index 000000000000..fa75acf23fe6
--- /dev/null
+++ b/biology/sra-tools/distinfo
@@ -0,0 +1,7 @@
+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
diff --git a/biology/sra-tools/files/Makefile.bsd b/biology/sra-tools/files/Makefile.bsd
new file mode 100644
index 000000000000..7692ec277948
--- /dev/null
+++ b/biology/sra-tools/files/Makefile.bsd
@@ -0,0 +1,72 @@
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+
+
+# default compiler
+ifeq (,$(COMP))
+	COMP = clang
+endif
+
+# handle attempts to set cross-compilation architecture
+# note that if your installation is set up for cross compilation,
+# you can try to enable it on your own.
+ifeq (i386,$(ARCH))
+i386:
+	@ true
+x86_64:
+	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
+endif
+
+ifeq (x86_64,$(ARCH))
+i386:
+	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
+x86_64:
+	@ true
+endif
+
+.PHONY: i386 x86_64
+
+
+# library prefix
+LPFX = lib
+
+# file extensions
+OBJX = o
+LOBX = pic.o
+LIBX = a
+SHLX = so
+
+# compilation defines
+DEFINES	:= -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS)
+
+# FreeBSD is a Unix variant; for most cases, linux sources do well
+OS_DAD = linux
+OS_GDAD = unix
+
+# flex+bison: on Mac, use source-controlled generated .c/.h files
+YACC = @ true
+LEX = @ true
+
+# build matrix
+COMPILERS = CLANG GCC
diff --git a/biology/sra-tools/files/byteswap.h b/biology/sra-tools/files/byteswap.h
new file mode 100644
index 000000000000..ef07fe98db64
--- /dev/null
+++ b/biology/sra-tools/files/byteswap.h
@@ -0,0 +1,40 @@
+/*===========================================================================
+*
+*                            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_
+
+#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 bswap_16(x) bswap16 (x)
+#define bswap_32(x) bswap32 (x)
+#define bswap_64(x) bswap64 (x)
+
+#endif /* _h_byteswap_ */
diff --git a/biology/sra-tools/files/ld.bsd.clang.sh b/biology/sra-tools/files/ld.bsd.clang.sh
new file mode 100755
index 000000000000..61c7779adcf1
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.clang.sh
@@ -0,0 +1,47 @@
+#!/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
diff --git a/biology/sra-tools/files/ld.bsd.cmn.sh b/biology/sra-tools/files/ld.bsd.cmn.sh
new file mode 100755
index 000000000000..a0a65f39884b
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.cmn.sh
@@ -0,0 +1,158 @@
+#!/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 $LD_REF_SYMBOLS"
+        LD_ALL_STATE=0
+    fi
+}
diff --git a/biology/sra-tools/files/ld.bsd.dlib.sh b/biology/sra-tools/files/ld.bsd.dlib.sh
new file mode 100755
index 000000000000..a74f2b006818
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.dlib.sh
@@ -0,0 +1,308 @@
+#!/usr/local/bin/bash
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+
+
+# ===========================================================================
+# input library types, and their handling
+#
+#  normal linkage
+#   -l : find shared or static
+#   -s : require static
+#   -d : require shared
+#
+#  static linkage
+#   -l : require static
+#   -s : require static
+#   -d : ignore
+# ===========================================================================
+
+
+# script name
+SELF_NAME="$(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 > "$TARG.md5"
+fi
diff --git a/biology/sra-tools/files/ld.bsd.exe.sh b/biology/sra-tools/files/ld.bsd.exe.sh
new file mode 100755
index 000000000000..650a212780c3
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.exe.sh
@@ -0,0 +1,326 @@
+#!/usr/local/bin/bash
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+
+
+# ===========================================================================
+# input library types, and their handling
+#
+#  normal linkage
+#   -l : find shared or static
+#   -s : require static
+#   -d : ignore - will be dynamically loaded
+#
+#  static linkage
+#   -l : require static
+#   -s : require static
+#   -d : require static
+# ===========================================================================
+
+
+# script name
+SELF_NAME="$(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 > "$TARG.md5"
+fi
diff --git a/biology/sra-tools/files/ld.bsd.gcc.sh b/biology/sra-tools/files/ld.bsd.gcc.sh
new file mode 100755
index 000000000000..61c7779adcf1
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.gcc.sh
@@ -0,0 +1,47 @@
+#!/usr/local/bin/bash
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+
+# define linker params
+LD_EXPORT_GLOBAL="-Wl,--export-dynamic"
+LD_MULTIPLE_DEFS="-Wl,-zmuldefs"
+LD_STATIC="-Wl,-Bstatic"
+LD_DYNAMIC="-Wl,-Bdynamic"
+LD_ALL_SYMBOLS="-Wl,-whole-archive"
+LD_REF_SYMBOLS="-Wl,-no-whole-archive"
+
+# build command
+DLIB_CMD="$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
diff --git a/biology/sra-tools/files/ld.bsd.ln.sh b/biology/sra-tools/files/ld.bsd.ln.sh
new file mode 100755
index 000000000000..4897950a2144
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.ln.sh
@@ -0,0 +1,98 @@
+#!/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
diff --git a/biology/sra-tools/files/ld.bsd.slib.sh b/biology/sra-tools/files/ld.bsd.slib.sh
new file mode 100755
index 000000000000..c0e85183ea4e
--- /dev/null
+++ b/biology/sra-tools/files/ld.bsd.slib.sh
@@ -0,0 +1,146 @@
+#!/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 > "$TARG.md5"
+fi
diff --git a/biology/sra-tools/files/patch-build_ld.linux.exe.sh b/biology/sra-tools/files/patch-build_ld.linux.exe.sh
new file mode 100644
index 000000000000..970a7e10aac8
--- /dev/null
+++ b/biology/sra-tools/files/patch-build_ld.linux.exe.sh
@@ -0,0 +1,11 @@
+--- build/ld.linux.exe.sh.orig	2021-06-20 16:32:05 UTC
++++ build/ld.linux.exe.sh
+@@ -313,6 +313,8 @@ then
+     fi
+ fi
+ 
++CMD="$CMD -lepoll-thread -lbz2 -lz"
++
+ # add in math library
+ if [ $HAVE_M -ne 0 ]
+ then
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang
new file mode 100644
index 000000000000..99878e619099
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.clang
@@ -0,0 +1,30 @@
+--- 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)
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env
new file mode 100644
index 000000000000..4e0b80a9bf78
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.env
@@ -0,0 +1,25 @@
+--- 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)
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc
new file mode 100644
index 000000000000..d2fc4c4e04c6
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.gcc
@@ -0,0 +1,35 @@
+--- 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):$(ILIBDIR)
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install
new file mode 100644
index 000000000000..143eb4d07868
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.install
@@ -0,0 +1,11 @@
+--- ncbi-vdb/build/Makefile.install.orig	2021-03-15 18:16:43 UTC
++++ ncbi-vdb/build/Makefile.install
+@@ -69,7 +69,7 @@ ifeq (1,$(HAVE_HDF5))
+ endif
+ 
+ 
+-LIB_TARGET = $(INST_LIBDIR)$(BITS)
++LIB_TARGET = $(INST_LIBDIR)
+ 
+ LIBRARIES_WITH_PREFIX = \
+ 	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell
new file mode 100644
index 000000000000..fb98fc610def
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_build_Makefile.shell
@@ -0,0 +1,31 @@
+--- 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
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h b/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h
new file mode 100644
index 000000000000..3edaa3fa3fb3
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_interfaces_os_sun_atomic32.h
@@ -0,0 +1,85 @@
+--- 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
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile
new file mode 100644
index 000000000000..4d3fae2846fd
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_ext_Makefile
@@ -0,0 +1,12 @@
+--- 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
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c
new file mode 100644
index 000000000000..f454a2b79c16
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c
@@ -0,0 +1,20 @@
+--- ncbi-vdb/libs/kfg/config.c.orig	2021-03-15 18:16:43 UTC
++++ ncbi-vdb/libs/kfg/config.c
+@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi
+     const char * std_locs [] =
+     {
+ #if ! WINDOWS
+-        "/etc/ncbi",
++        @@PREFIX@@ "/etc/ncbi",
+ #else
+         "/c/ncbi",
+ #endif
+@@ -2850,6 +2850,8 @@ void add_predefined_nodes ( KConfig * self, const char
+     #define OS "win"
+ #elif SUN
+     #define OS "sun"
++#elif BSD
++    #define OS "bsd"
+ #else
+     #error unrecognized OS
+ #endif
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c
new file mode 100644
index 000000000000..3732c47ce93a
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c
@@ -0,0 +1,11 @@
+--- ncbi-vdb/libs/klib/unix/systime.c.orig	2017-07-14 21:55:36 UTC
++++ ncbi-vdb/libs/klib/unix/systime.c
+@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co
+         t . tm_isdst = self -> dst;
+ 
+         ts = mktime ( &t );
+-        ts -= timezone;
++        ts += localtime(&ts)->tm_gmtoff;
+     }
+ 
+     return ts;
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c
new file mode 100644
index 000000000000..50484bb1d503
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c
@@ -0,0 +1,10 @@
+--- ncbi-vdb/libs/kns/unix/syssock.c.orig	2017-07-14 21:55:36 UTC
++++ ncbi-vdb/libs/kns/unix/syssock.c
+@@ -66,6 +66,7 @@
+ #include <sys/types.h>
+ #include <sys/socket.h>
+ #include <sys/un.h>
++#include <netinet/in.h>
+ #include <netinet/tcp.h>
+ #include <poll.h>
+ #include <unistd.h>
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile
new file mode 100644
index 000000000000..7f5ad0a8802f
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile
@@ -0,0 +1,20 @@
+--- 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)/*
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile
new file mode 100644
index 000000000000..b1c52cb7ecf4
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_search_Makefile
@@ -0,0 +1,12 @@
+--- ncbi-vdb/libs/search/Makefile.orig	2017-07-14 21:55:36 UTC
++++ ncbi-vdb/libs/search/Makefile
+@@ -39,6 +39,9 @@ OBJFILES = \
+ 
+ include $(TOP)/build/Makefile.env
+ 
++CARCH += -msse2
++# nucstrstr.c requires SSE2
++
+ #-------------------------------------------------------------------------------
+ # outer targets
+ #
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl b/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl
new file mode 100644
index 000000000000..8d293bbd71cc
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_setup_konfigure.perl
@@ -0,0 +1,243 @@
+--- ncbi-vdb/setup/konfigure.perl.orig	2021-03-15 18:16:43 UTC
++++ ncbi-vdb/setup/konfigure.perl
+@@ -192,7 +192,7 @@ if ($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;
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl b/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl
new file mode 100644
index 000000000000..01cb9824ff7b
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_setup_os-arch.prl
@@ -0,0 +1,20 @@
+--- 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';
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh b/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh
new file mode 100644
index 000000000000..ebc81bd3fc5b
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh
@@ -0,0 +1,49 @@
+--- ncbi-vdb/test/kapp/run-sig-core.sh.orig	2017-10-27 07:23:08 UTC
++++ ncbi-vdb/test/kapp/run-sig-core.sh
+@@ -29,12 +29,12 @@ BUILD_TYPE="$3"
+ 
+ SIGQUIT=3
+ 
+-function killFromBackground ()
++killFromBackground ()
+ {
+     PARENT_PID=$1
+     for I in 1 2 3 4 5
+     do
+-        COMMAND="ps -ef|awk '\$3==${PARENT_PID} && \$8==\"${BINARY_PATH}\"  {print \$2}'"
++        COMMAND="ps awwo pid,ppid,command|awk '\$2==${PARENT_PID} && \$3==\"${BINARY_PATH}\"  {print \$1}'"
+         eval PID=\`${COMMAND}\`
+         if [ "$PID" = "" ]; then
+             sleep 1
+@@ -44,7 +44,7 @@ function killFromBackground ()
+     done
+ 
+     if [ "$PID" != "" ]; then
+-        kill -s $SIGQUIT $PID
++        kill -s QUIT $PID
+     fi
+ 
+     echo $PID > killed.pid
+@@ -63,6 +63,13 @@ if [ "$HOST_OS" = "mac" ]; then
+    fi
+ 
+    CORE_FOLDER="/core/"
++elif [ "$HOST_OS" = "bsd" ]; then
++   if [ "`ulimit -c`" = "0" ] || [ "`/sbin/sysctl -n kern.coredump`" != "1" ]; then
++       echo "Core files are disabled. Skipping core file tests"
++       exit 0
++   fi
++
++   CORE_FOLDER="./"
+ elif [ "$HOST_OS" = "linux" ]; then
+    if [ "`ulimit -c`" = "0" ]; then
+        echo "Core files are disabled. Skipping core file tests"
+@@ -92,7 +99,7 @@ wait
+ BINARY_PID=`cat killed.pid`
+ rm killed.pid
+ 
+-CORE_FILE="${CORE_FOLDER}core.${BINARY_PID}"
++CORE_FILE="${CORE_FOLDER}${BINARY_PATH##*/}.core"
+ 
+ if [ "$BUILD_TYPE" = "dbg" ]; then
+    if [ -f $CORE_FILE ]; then
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp
new file mode 100644
index 000000000000..468483b89535
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp
@@ -0,0 +1,11 @@
+--- ncbi-vdb/test/kfg/kfgtest.cpp.orig	2019-08-20 18:27:10 UTC
++++ ncbi-vdb/test/kfg/kfgtest.cpp
+@@ -280,6 +280,8 @@ FIXTURE_TEST_CASE(predef_OS, KfgFixture)
+     CreateAndLoad(GetName(), "var=$(OS)\n");
+     #if LINUX
+         #define OS "linux"
++    #elif BSD
++        #define OS "bsd"    
+     #elif SUN
+         #define OS "sun"
+     #elif MAC
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c b/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c
new file mode 100644
index 000000000000..76b1210a7ae7
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c
@@ -0,0 +1,11 @@
+--- ncbi-vdb/test/klib/printf-test.c.orig	2019-08-20 18:27:10 UTC
++++ ncbi-vdb/test/klib/printf-test.c
+@@ -503,7 +503,7 @@ rc_t run ( const char *progname )
+         if ( rc == 0 )
+         {
+             rc = make_initial_test ( field_width, precision, " ", "s", "Kurt is having a fit" );
+-#if !defined(__SunOS)  &&  !defined(__sun__)
++#if !defined(__SunOS)  &&  !defined(__sun__) && !defined(__FreeBSD__)
+             /* Solaris printf doesn't cope with NULLs */
+             rc = make_initial_test ( field_width, precision, " ", "s", NULL );
+ #endif            
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile b/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile
new file mode 100644
index 000000000000..958399985cc9
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_kns_Makefile
@@ -0,0 +1,19 @@
+--- 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
+ 
+ #----------------------------------------------------------------
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp
new file mode 100644
index 000000000000..52bcf0460632
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies.cpp
@@ -0,0 +1,11 @@
+--- 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"
diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp
new file mode 100644
index 000000000000..12780a95a08a
--- /dev/null
+++ b/biology/sra-tools/files/patch-ncbi-vdb_test_vfs_redirect-rejected-names-cgi-http-to-https.cpp
@@ -0,0 +1,11 @@
+--- 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
diff --git a/biology/sra-tools/files/patch-setup_install.perl b/biology/sra-tools/files/patch-setup_install.perl
new file mode 100644
index 000000000000..cc2eade52c15
--- /dev/null
+++ b/biology/sra-tools/files/patch-setup_install.perl
@@ -0,0 +1,13 @@
+--- 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} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";"
diff --git a/biology/sra-tools/files/patch-setup_konfigure.perl b/biology/sra-tools/files/patch-setup_konfigure.perl
new file mode 100644
index 000000000000..aacfe898be6d
--- /dev/null
+++ b/biology/sra-tools/files/patch-setup_konfigure.perl
@@ -0,0 +1,121 @@
+--- setup/konfigure.perl.orig	2021-03-15 18:25:25 UTC
++++ setup/konfigure.perl
+@@ -204,7 +204,7 @@ print "checking system type... " unless ($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) {
diff --git a/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c b/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c
new file mode 100644
index 000000000000..9b78a578a601
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c
@@ -0,0 +1,10 @@
+--- 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>
diff --git a/biology/sra-tools/files/patch-tools_copycat_Makefile b/biology/sra-tools/files/patch-tools_copycat_Makefile
new file mode 100644
index 000000000000..fb24ac9e5d4e
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_copycat_Makefile
@@ -0,0 +1,11 @@
+--- 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)
diff --git a/biology/sra-tools/files/patch-tools_driver-tool_Makefile b/biology/sra-tools/files/patch-tools_driver-tool_Makefile
new file mode 100644
index 000000000000..408b82819a43
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_driver-tool_Makefile
@@ -0,0 +1,16 @@
+--- 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 $@ $^ $(SRATOOLS_LIB)
diff --git a/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp b/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp
new file mode 100644
index 000000000000..46747e4840e5
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_driver-tool_cmdline.cpp
@@ -0,0 +1,13 @@
+--- tools/driver-tool/cmdline.cpp.orig	2021-04-21 19:42:12 UTC
++++ tools/driver-tool/cmdline.cpp
+@@ -50,6 +50,10 @@
+ #define environ (*_NSGetEnviron())
+ #endif
+ 
++#if defined(__FreeBSD__)
++extern char **environ;
++#endif
++
+ #define TRACE( lvl, ... ) /* ignore */
+ 
+ namespace ncbi
diff --git a/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile b/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile
new file mode 100644
index 000000000000..c5c827645c95
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_driver-tool_utf8proc_Makefile
@@ -0,0 +1,11 @@
+--- tools/driver-tool/utf8proc/Makefile.orig	2021-04-29 14:50:48 UTC
++++ tools/driver-tool/utf8proc/Makefile
+@@ -79,7 +79,7 @@ libutf8proc.a: utf8proc.o
+ 
+ libutf8proc.so.$(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) $@
diff --git a/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c b/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c
new file mode 100644
index 000000000000..0a8f0fd3ccb1
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_fastq-loader_spot-assembler.c
@@ -0,0 +1,11 @@
+--- 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>
+ 
diff --git a/biology/sra-tools/files/patch-tools_sra-sort_Makefile b/biology/sra-tools/files/patch-tools_sra-sort_Makefile
new file mode 100644
index 000000000000..8e96b1a43f97
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_sra-sort_Makefile
@@ -0,0 +1,13 @@
+--- 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)
diff --git a/biology/sra-tools/files/patch-tools_util_validate-names4.c b/biology/sra-tools/files/patch-tools_util_validate-names4.c
new file mode 100644
index 000000000000..5d66976db304
--- /dev/null
+++ b/biology/sra-tools/files/patch-tools_util_validate-names4.c
@@ -0,0 +1,13 @@
+--- 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)
diff --git a/biology/sra-tools/pkg-descr b/biology/sra-tools/pkg-descr
new file mode 100644
index 000000000000..e9324dc5a96a
--- /dev/null
+++ b/biology/sra-tools/pkg-descr
@@ -0,0 +1,18 @@
+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.
+
+WWW: https://github.com/ncbi/sra-tools/wiki
diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist
new file mode 100644
index 000000000000..dad924be78f4
--- /dev/null
+++ b/biology/sra-tools/pkg-plist
@@ -0,0 +1,57 @@
+bin/abi-dump
+bin/abi-load
+bin/align-cache
+bin/align-info
+bin/bam-load
+bin/cache-mgr
+bin/ccextract
+bin/cg-load
+bin/check-corrupt
+bin/copycat
+bin/fasterq-dump
+bin/fastq-dump
+bin/fastq-load
+bin/helicos-load
+bin/illumina-dump
+bin/illumina-load
+bin/kar
+bin/kar+
+bin/kar+meta
+bin/kdb-index
+bin/kdbmeta
+bin/kget
+bin/latf-load
+bin/make-read-filter
+bin/md5cp
+bin/ngs-pileup
+bin/pacbio-correct
+bin/pacbio-loadxml
+bin/prefetch
+bin/qual-recalib-stat
+bin/rcexplain
+bin/read-filter-redact
+bin/sam-dump
+bin/samview
+bin/schema-replace
+bin/sff-dump
+bin/sff-load
+bin/sra-pileup
+bin/sra-sort
+bin/sra-sort-cg
+bin/sra-stat
+bin/srapath
+bin/sratools
+bin/srf-load
+bin/test-read-write-cursor
+bin/test-sra
+bin/vdb-config
+bin/vdb-copy
+bin/vdb-decrypt
+bin/vdb-diff
+bin/vdb-dump
+bin/vdb-encrypt
+bin/vdb-lock
+bin/vdb-passwd
+bin/vdb-sql
+bin/vdb-unlock
+bin/vdb-validate
author	Jason W. Bacon <jwb@FreeBSD.org>	2021-06-22 17:55:15 +0000
committer	Jason W. Bacon <jwb@FreeBSD.org>	2021-06-22 17:55:15 +0000
commit	69656bf0d7d99660e536c22472a5eae639695a97 (patch)
tree	1eec14b05b8f280276d6e0dbc1063d9f91d4a327 /biology
parent	754ca6f4c9c3c1ce86e13bdf62db3e3282346cbf (diff)
download	ports-69656bf0d7d99660e536c22472a5eae639695a97.tar.gz ports-69656bf0d7d99660e536c22472a5eae639695a97.zip