diff --git a/Makefile b/Makefile
index d10dd35ad..8f184a9ee 100644
--- a/Makefile
+++ b/Makefile
@@ -23,166 +23,5 @@
 # ===========================================================================
 
 
-#-------------------------------------------------------------------------------
-# environment
-#
-TOP ?= $(CURDIR)
-include $(TOP)/build/Makefile.shell
-
-
-#-------------------------------------------------------------------------------
-# default
-#
-SUBDIRS = \
-	shared \
-	tools \
-	ngs \
-
-# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
-include $(TOP)/build/Makefile.targets
-
-default: $(SUBDIRS)
-
-test: all
-
-$(SUBDIRS) test:
-	@ $(MAKE) -C $@
-
-.PHONY: default $(SUBDIRS) test
-
-#-------------------------------------------------------------------------------
-# all
-#
-$(SUBDIRS_ALL):
-
-#-------------------------------------------------------------------------------
-# std
-#
-$(SUBDIRS_STD):
-
-#-------------------------------------------------------------------------------
-# install
-#
-install install-delite:
-	@ echo "Checking make status of tools..."
-	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) std
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install $@
-
-uninstall:    
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
-
-.PHONY: install uninstall
-
-#-------------------------------------------------------------------------------
-# clean
-#
-clean: clean_deb clean_rpm clean_test
-
-clean_test:
-	@ $(MAKE) -s -C test clean
-
-#-------------------------------------------------------------------------------
-# runtests
-#
-runtests: runtests_test
-
-runtests_test:
-	@ $(MAKE) -s -C test runtests
-
-#	@ $(MAKE) -s -C ngs runtests
-
-#-------------------------------------------------------------------------------
-# slowtests
-#
-slowtests: slowtests_test
-
-slowtests_test:
-	@ $(MAKE) -s -C test slowtests
-
-#-------------------------------------------------------------------------------
-# valgrind
-#
-valgrind: valgrind_test
-
-valgrind_test:
-	@ $(MAKE) -s -C test valgrind
-
-#-------------------------------------------------------------------------------
-# RPM
-#
-ifeq (mac,$(OS))
-rpm:
-	@ echo "Not making rpm on Mac"
-clean_rpm:
-else
-rpm: std
-	@ $(MAKE)       rpm -s TOP=$(CURDIR) -f build/Makefile.rpm
-clean_rpm:
-	@ $(MAKE) clean_rpm -s TOP=$(CURDIR) -f build/Makefile.rpm
-endif
-
-#-------------------------------------------------------------------------------
-# DEB
-#
-ifeq (mac,$(OS))
-deb: std
-else
-deb:
-endif
-	@ $(MAKE)       deb -s TOP=$(CURDIR) -f build/Makefile.deb
-clean_deb:
-	@ $(MAKE) clean_deb -s TOP=$(CURDIR) -f build/Makefile.deb
-
-#-------------------------------------------------------------------------------
-# pass-through targets
-#
-COMPILERS = GCC ICC VC++ CLANG
-ARCHITECTURES = i386 x86_64 sparc32 sparc64
-CONFIG = debug profile release
-PUBLISH = scm pubtools
-REPORTS = bindir targdir osdir config compilers architecture architectures
-PASSTHRUS = \
-	out \
-	CC $(COMPILERS) \
-	$(ARCHITECTURES) \
-	$(CONFIG) $(PUBLISH) \
-	purify purecov \
-	local static dynamic
-
-$(RHOSTS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env local
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env require-proxy-exec
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
-
-$(PASSTHRUS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
-
-$(REPORTS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
-
-.PHONY: $(PASSTHRUS) $(RHOSTS) $(REPORTS)
-
-
-#-------------------------------------------------------------------------------
-# configuration help
-#
-help configure:
-	@ echo "Before initial build, run './configure --build-prefix=<out>' from"
-	@ echo "the project root to set the output directory of your builds."
-	@ echo
-	@ echo "To select a compiler, run 'make <comp>' where"
-	@ echo "comp = { "$(COMPILERS)" }."
-	@ echo
-	@ echo "For hosts that support cross-compilation ( only Macintosh today ),"
-	@ echo "you can run 'make <arch>' where arch = { "$(ARCHITECTURES)" }."
-	@ echo
-	@ echo "To set a build configuration, run 'make <config>' where"
-	@ echo "config = { "$(CONFIG)" }."
-	@ echo
-	@ echo "To select a remote build configuration, run 'make <rhost>' where"
-	@ echo "rhost = { "$(RHOSTS)" }."
-	@ echo
-
-.PHONY: help configure
+TOP ?= $(shell pwd)
+include $(TOP)/build/Makefile.env
\ No newline at end of file
diff --git a/Makefile.old b/Makefile.old
new file mode 100644
index 000000000..d10dd35ad
--- /dev/null
+++ b/Makefile.old
@@ -0,0 +1,188 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+#-------------------------------------------------------------------------------
+# environment
+#
+TOP ?= $(CURDIR)
+include $(TOP)/build/Makefile.shell
+
+
+#-------------------------------------------------------------------------------
+# default
+#
+SUBDIRS = \
+	shared \
+	tools \
+	ngs \
+
+# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
+include $(TOP)/build/Makefile.targets
+
+default: $(SUBDIRS)
+
+test: all
+
+$(SUBDIRS) test:
+	@ $(MAKE) -C $@
+
+.PHONY: default $(SUBDIRS) test
+
+#-------------------------------------------------------------------------------
+# all
+#
+$(SUBDIRS_ALL):
+
+#-------------------------------------------------------------------------------
+# std
+#
+$(SUBDIRS_STD):
+
+#-------------------------------------------------------------------------------
+# install
+#
+install install-delite:
+	@ echo "Checking make status of tools..."
+	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) std
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install $@
+
+uninstall:    
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
+
+.PHONY: install uninstall
+
+#-------------------------------------------------------------------------------
+# clean
+#
+clean: clean_deb clean_rpm clean_test
+
+clean_test:
+	@ $(MAKE) -s -C test clean
+
+#-------------------------------------------------------------------------------
+# runtests
+#
+runtests: runtests_test
+
+runtests_test:
+	@ $(MAKE) -s -C test runtests
+
+#	@ $(MAKE) -s -C ngs runtests
+
+#-------------------------------------------------------------------------------
+# slowtests
+#
+slowtests: slowtests_test
+
+slowtests_test:
+	@ $(MAKE) -s -C test slowtests
+
+#-------------------------------------------------------------------------------
+# valgrind
+#
+valgrind: valgrind_test
+
+valgrind_test:
+	@ $(MAKE) -s -C test valgrind
+
+#-------------------------------------------------------------------------------
+# RPM
+#
+ifeq (mac,$(OS))
+rpm:
+	@ echo "Not making rpm on Mac"
+clean_rpm:
+else
+rpm: std
+	@ $(MAKE)       rpm -s TOP=$(CURDIR) -f build/Makefile.rpm
+clean_rpm:
+	@ $(MAKE) clean_rpm -s TOP=$(CURDIR) -f build/Makefile.rpm
+endif
+
+#-------------------------------------------------------------------------------
+# DEB
+#
+ifeq (mac,$(OS))
+deb: std
+else
+deb:
+endif
+	@ $(MAKE)       deb -s TOP=$(CURDIR) -f build/Makefile.deb
+clean_deb:
+	@ $(MAKE) clean_deb -s TOP=$(CURDIR) -f build/Makefile.deb
+
+#-------------------------------------------------------------------------------
+# pass-through targets
+#
+COMPILERS = GCC ICC VC++ CLANG
+ARCHITECTURES = i386 x86_64 sparc32 sparc64
+CONFIG = debug profile release
+PUBLISH = scm pubtools
+REPORTS = bindir targdir osdir config compilers architecture architectures
+PASSTHRUS = \
+	out \
+	CC $(COMPILERS) \
+	$(ARCHITECTURES) \
+	$(CONFIG) $(PUBLISH) \
+	purify purecov \
+	local static dynamic
+
+$(RHOSTS):
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env local
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env require-proxy-exec
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
+
+$(PASSTHRUS):
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
+
+$(REPORTS):
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+
+.PHONY: $(PASSTHRUS) $(RHOSTS) $(REPORTS)
+
+
+#-------------------------------------------------------------------------------
+# configuration help
+#
+help configure:
+	@ echo "Before initial build, run './configure --build-prefix=<out>' from"
+	@ echo "the project root to set the output directory of your builds."
+	@ echo
+	@ echo "To select a compiler, run 'make <comp>' where"
+	@ echo "comp = { "$(COMPILERS)" }."
+	@ echo
+	@ echo "For hosts that support cross-compilation ( only Macintosh today ),"
+	@ echo "you can run 'make <arch>' where arch = { "$(ARCHITECTURES)" }."
+	@ echo
+	@ echo "To set a build configuration, run 'make <config>' where"
+	@ echo "config = { "$(CONFIG)" }."
+	@ echo
+	@ echo "To select a remote build configuration, run 'make <rhost>' where"
+	@ echo "rhost = { "$(RHOSTS)" }."
+	@ echo
+
+.PHONY: help configure
diff --git a/build/Makefile.env b/build/Makefile.env
index af853be38..fe7306936 100644
--- a/build/Makefile.env
+++ b/build/Makefile.env
@@ -22,403 +22,131 @@
 #
 # ===========================================================================
 
-# pick up dependencies from object directory
-ifdef SRCDIR
-	include $(wildcard *.d)
-endif
+default all std: makedirs cmake
 
 # determine shell environment
-include $(TOP)/build/Makefile.shell
-
-# load build configuration
-include $(CONFIG_FILE)
-
-# normally build shared and static external libs
-LIBEXT = $(LIBX) $(SHLX)
-
-# normally build static intermediate libs
-ILIBEXT = $(LIBX)
-
-# determine BUILD
-ifeq (,$(BUILD))
-	BUILD = dbg
-endif
-
-# some rules are sensitive to the type of build
-BUILDTYPE = $(BUILD)
-
-# adjust settings for build
-ifeq (dbg,$(BUILD))
-	DEBUG := -D_DEBUGGING
-endif
-ifeq (prof,$(BUILD))
-	DEBUG := -D_PROFILING
-endif
-ifeq (pur,$(BUILD))
-	DEBUG := -D_DEBUGGING
-	LD_PRE := purify
-	LNKG = stat
-endif
-ifeq (pcov,$(BUILD))
-	DEBUG := -D_DEBUGGING
-	LD_PRE := purecov
-	LNKG = stat
+CONFIG_FILE = $(TOP)/build/Makefile.config
+ifeq (no, $(shell test -f $(CONFIG_FILE) && echo yes || echo no))
+    $(error "*** File '$(CONFIG_FILE)' is missing. Please run $(TOP)/build/configure")
 endif
-ifeq (scm,$(BUILD))
-	BUILDTYPE = rel
-	CHECKSUM := --checksum
-endif
-
-ifeq (yes,$(HAS_RHOST))
-	LOCAL_OR_REMOTE = remote
-else
-	LOCAL_OR_REMOTE = local
-endif
-
-# pre-built sra-tools are static
-ifeq (1,$(WANTS_STATIC))
-	STATIC = --static
-	STATICSYSLIBS = --static-system-libs
-endif
-
-# drop all suffix rules
-.SUFFIXES:
-
-# load OS and COMP specific files
-include $(TOP)/build/Makefile.$(OS)
-include $(TOP)/build/Makefile.$(COMP)
-include $(TOP)/build/Makefile.rules
-
-# external schema modules
-EXT_SCHEMA_MODULES = axf sraxf wgsxf vxf
-UPDATE_SCHEMA_LIBS := $(addprefix -lw,$(EXT_SCHEMA_MODULES))
-READONLY_SCHEMA_LIBS = $(addprefix -l,$(EXT_SCHEMA_MODULES))
-ALWAYS_STATIC_SCHEMA_LIBS = $(addprefix -s,$(EXT_SCHEMA_MODULES))
-
-# full directory paths
-TARGDIR ?= $(OUTDIR)/$(OS)/$(TOOLSET)/$(ARCH)/$(BUILD)
-BINDIR ?= $(TARGDIR)/bin
-ifeq (win,$(OS))
-    # on Windows, place test executables next to .dlls
-    TEST_BINDIR = $(BINDIR)
-else
-    TEST_BINDIR = $(TARGDIR)/test-bin
-endif
-ILIBDIR = $(TARGDIR)/ilib
-LIBDIR = $(TARGDIR)/lib
-OBJDIR = $(TARGDIR)/obj/$(MODULE)
-
-CLSPATH         ?= $(TARGDIR)/java
-CLASSPATH       ?= $(CLSPATH)
-CLASSDIR        ?= $(TARGDIR)/$(MODULE)
-TEST_CLSPATH    ?= $(OUTDIR)/test/java
-JAVASOURCEPATH  ?= $(TOP)/java
 
-# path to the ncbi sub-directory
-# this is where modules and installed schema files are kept
-ifeq (win,$(OS))
-    # under Windows, we are always relative to binary path
-	NCBIDIR = $(BINDIR)/ncbi
+# determine SRCDIR
+ifdef MODULE
+    SRCDIR=$(TOP)/$(MODULE)
 else
-	# under Linux and Mac, it can be binary or library
-	NCBIDIR = $(LIBDIR)/ncbi $(BINDIR)/ncbi
+    SRCDIR=$(TOP)/
 endif
 
-DEFAULT_CRT = $(VDB_SRCDIR)/libs/kfg/certs.kfg
-DEFAULT_KFG = $(VDB_SRCDIR)/libs/kfg/default.kfg
-
-# make reissue command
-MAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
-    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile
-
-JMAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
-    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(CLASSDIR) -f $(SRCDIR)/Makefile
+# load build configuration
+CURDIR = $(SRCDIR)
+include $(CONFIG_FILE)
 
-# directory and link creation
-SUBDIRS = bin test-bin ilib lib
-OUTDIRS = schema
+TEST_BINDIR = $(TARGDIR)/test-bin
 
 # clean rules
-stdclean:
-	@ -rm -rf $(OBJDIR)
-	@ -rm -rf $(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \
-			$(addsuffix .*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
-			$(addsuffix -static.*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
-			$(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS))) \
-			$(addsuffix *,$(addprefix $(TEST_BINDIR)/,$(ALL_TOOLS) $(TEST_TOOLS)))
-
-stdjclean:
-	@ -rm -rf $(CLSPATH) $(CLSDIR)
-
-# removing symbolic links that point to specific builds
-removelinks:
-	@ test ! -h $(OUTDIR)/schema && rm -rf $(OUTDIR)/schema || true
-	@ rm -f $(addprefix $(OUTDIR)/,$(addsuffix $(BITS),$(SUBDIRS)))
-	@ rm -f $(addprefix $(OUTDIR)/,$(OUTDIRS))
-
-$(BINDIR)/ncbi/certs.kfg: $(DEFAULT_CRT)
-	@ mkdir -p $(NCBIDIR)
-	@ cp -v $(DEFAULT_CRT) $@
-
-$(BINDIR)/ncbi/default.kfg: $(DEFAULT_KFG)
-	@ mkdir -p $(NCBIDIR)
-	@ cp -v $(DEFAULT_KFG) $@
-
-# create all required output directories
-makedirs: $(BINDIR)/ncbi/certs.kfg $(BINDIR)/ncbi/default.kfg
-	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
-
-makejdirs:
-	@ mkdir -p $(CLASSDIR) $(CLSDIR)
-
-# build version include files
-vers-includes: makedirs
-	@ $(MAKE_CMD) -s $(TARGDIR)/$@
-
-ifeq (win,$(OS))
-
-# Windows doesn't really support symbolic links
-# we may add them back in when our toolkit is able to create them
-rebuild-dirlinks: makedirs
-	@ true
-else
-
-LNDIRS = $(addprefix ln_,$(SUBDIRS))
-$(LNDIRS):
-	@ ln -s $(TARGDIR)/$(subst ln_,,$@) $(OUTDIR)/$(subst ln_,,$@)$(BITS)
-
-ifdef NOREBUILD_LINKS
-rebuild-dirlinks:
-	@ true
-else
-rebuild-dirlinks: removelinks makedirs $(LNDIRS)
-	@ ln -s $(VDB_INCDIR) $(OUTDIR)/schema
-endif
-
-endif
-
-.PHONY: stdclean removelinks makedirs vers-includes rebuild-dirlinks
-.PHONY: stdjclean makejdirs
-
-# configuration targets
-out:
-	@ echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(BUILD_OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
-
-$(RHOSTS):
-	@ cat $(TOP)/rhosts/$@ >> $(TOP)/build/RHOST.$(HOST_OS)
-
-require-proxy-exec:
-	@ $(MAKE) -C $(TOP)/test/proxy_exec proxy-exec
-	@ echo "PROXY_TOOL := $(BINDIR)/proxy-exec" > $(TOP)/build/RHOST.$(HOST_OS)
-
-local:
-	@ rm -f $(TOP)/build/RHOST.$(HOST_OS)
-
-CC:
-	@ echo cc > $(TOP)/build/COMP.$(OS)
-
-GCC:
-	@ echo gcc > $(TOP)/build/COMP.$(OS)
-
-ICC:
-	@ echo icc > $(TOP)/build/COMP.$(OS)
-
-VC++:
-	@ echo vc++ > $(TOP)/build/COMP.$(OS)
-
-CLANG:
-	@ echo clang > $(TOP)/build/COMP.$(OS)
-
-static dynamic:
-	@ echo "there is no longer any difference between static and dynamic builds"
-
-debug:
-	@ echo dbg > $(TOP)/build/BUILD.$(OS)
-
-profile:
-	@ echo prof > $(TOP)/build/BUILD.$(OS)
-
-release:
-	@ echo rel > $(TOP)/build/BUILD.$(OS)
-
-scm:
-	@ echo scm > $(TOP)/build/BUILD.$(OS)
-
-pubtools: release
-
-bindir:
-	@ echo "$(BINDIR)"
-
-targdir:
-	@ echo "$(TARGDIR)"
-
-osdir:
-	@ echo "$(OUTDIR)/$(OS)"
-
-compilers:
-	@ echo "$(COMPILERS)"
-
-architectures:
-	@ echo "$(ARCHITECTURES)"
-
-architecture:
-	@ echo "$(ARCH)"
+clean:
+	-rm -rf $(OBJDIR) $(ILIBDIR) $(LIBDIR) $(BINDIR) $(TEST_BINDIR)
 
 config:
-	@ echo "  current build is $(LOCAL_OR_REMOTE) $(BUILD_OS) $(BUILD) $(ARCH) build using $(TOOLSET) tools"
-	@ echo "  output target directory is '$(TARGDIR)'"
+	@ echo "Current configuration: $(CONFIGURED)"
+	@ echo "CMake build directory: '$(TARGDIR)/obj'"
+	@ echo "Output target directory: '$(TARGDIR)'"
+	@ echo "Installation target directory: '$(INST_LIBDIR)'"
 	@ echo
 
-purify:
-	@ echo pur > $(TOP)/build/BUILD.$(OS)
-
-purecov:
-	@ echo pcov > $(TOP)/build/BUILD.$(OS)
-
-.PHONY: out CC GCC ICC debug profile release scm purify purecov local local require-proxy-exec $(RHOSTS) bindir report_config
-
-# includes based upon build
-ITF   = $(VDB_INCDIR)/
-OSINC = $(VDB_INCDIR)/os
-CCINC = $(VDB_INCDIR)/cc
-XTINC = $(VDB_INCDIR)/ext
-NGSINC = $(NGS_INCDIR)
-OVERRIDEINC = $(TOP)/interfaces/override
-
-# OS specific source and include dirs
-SRCDIRS_OS = $(SRCDIR)/$(OS)
-INCDIRS_OS = $(OSINC)/$(OS)
-
-# most OS' have a parent type
-ifdef OS_DAD
-
-SRCDIRS_OS += $(SRCDIR)/$(OS_DAD)
-INCDIRS_OS += $(OSINC)/$(OS_DAD)
-
-# some OS' have a grandparent
-ifdef OS_GDAD
-SRCDIRS_OS += $(SRCDIR)/$(OS_GDAD)
-INCDIRS_OS += $(OSINC)/$(OS_GDAD)
-endif
+#-------------------------------------------------------------------------------
+# CMake bridge
+#
 
+ifeq (dbg,$(BUILD))
+    CMAKE_BUILD = Debug
+else
+    CMAKE_BUILD = Release
 endif
 
-# compiler specific includes
-INCDIRS_COMP = \
-	$(CCINC)/$(COMP)/$(ARCH) \
-	$(CCINC)/$(COMP)
+unexport TOP SRCDIR
 
-# some compilers have a parent type
-ifdef COMP_DAD
+# CPP comes from Makefile.config.$(OS_ARCH)
+# TODO: simplify Makefile.config.$(OS_ARCH) generated by ./configure - switch from using LD to a new variable
+CMAKEFLAGS = \
+    -DTARGDIR=$(TARGDIR)                        \
+    -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=$(ILIBDIR) \
+    -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=$(LIBDIR)  \
+    -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=$(BINDIR)  \
+    -DCMAKE_BUILD_TYPE=$(CMAKE_BUILD)           \
+    -DCMAKE_INSTALL_PREFIX=$(INST_BINDIR)/..    \
+    -DCMAKE_C_COMPILER=$(shell which $(LD))     \
+    -DCMAKE_CXX_COMPILER=$(shell which $(CPP))  \
+    -DVDB_BINDIR=$(VDB_LIBDIR)/.. \
+	-DPYTHON_PATH=$(PYTHON)
 
-INCDIRS_COMP += \
-	$(CCINC)/$(COMP_DAD)/$(ARCH) \
-	$(CCINC)/$(COMP_DAD)
+makedirs:
+	mkdir -p $(TARGDIR)/obj
 
-endif
+cmake_only:
+	cd $(TARGDIR)/obj; cmake $(CMAKEFLAGS) $(TOP)
 
-VPATH = \
-	$(SRCDIR)/$(COMP)/$(ARCH) \
-	$(SRCDIR)/$(COMP) \
-	$(SRCDIRS_OS) \
-	$(SRCDIR)
+cmake: makedirs cmake_only
+	+ make -C $(OBJDIR) --no-print-directory
 
-INCDIRS = \
-	$(addprefix -I,$(OVERRIDEINC)) \
-	$(addprefix -I,$(SRCDIRS_OS)) \
-	$(addprefix -I,$(SRCDIR) $(ITF)) \
-	$(addprefix -I,$(INCDIRS_COMP)) \
-	$(addprefix -I,$(INCDIRS_OS)) \
-	$(addprefix -I,$(XTINC) $(NGSINC)) \
-	-I.
+ctest: cmake
+	cd $(OBJDIR); ctest $(CMAKEFLAGS) --build-exe-dir $(BINDIR) $(CTESTARGS) -E "^SlowTest_" --verbose
 
+ctestall: cmake
+	cd $(OBJDIR); ctest $(CMAKEFLAGS) --build-exe-dir $(BINDIR) $(CTESTARGS) --verbose
 
-# linker paths
-LDPATHS =
+cinstall: cmake
+	+ make -C $(TARGDIR)/obj install
 
-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
+test runtests: ctest
 
+slowtests: ctestall
 
-# defines that describe os & architecture
-DLLX ?= $(SHLX)
-ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
-
-# default tool parameters
-CFLAGS	= -std=c11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-CPFLAGS = -std=c++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
+.PHONY: cmake_only cmake ctest ctestall test runtests slowtests
 
 #-------------------------------------------------------------------------------
-# runtests
-#
-# MallocScribble=1 is for catching allocation problems on Mac
+# install
 #
-HOSTNAME = $(shell hostname)
-WHICHASCP = $(shell which ascp 2> /dev/null)
-HAVE_NCBI_ASCP=1
-ifeq (,${WHICHASCP})
-	HAVE_NCBI_ASCP=
-endif
-ifeq (iebdev21,${HOSTNAME})
-	HAVE_NCBI_ASCP=
-endif
-
-ifeq ($(RUNTESTS_OVERRIDE),)
-runtests: all $(TEST_TOOLS)
-	@ export VDB_CONFIG=$(VDB_CONFIG);export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\
-	for i in $(TEST_TOOLS);\
-	do\
-		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
-		echo Run VDB_CONFIG=$$VDB_CONFIG $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
-		if [ "$$r" != "0" ] ; then exit $$r; fi; \
-	done
+install: cinstall
 
-.PHONY: runtests
-endif
+.PHONY: install
 
 #-------------------------------------------------------------------------------
-# slowtests
+# help
 #
-# $(SLOWTESTSDATADIR) should be used to create temporary test files
-SLOWTESTSDATADIR ?= /panfs/pan1.be-md.ncbi.nlm.nih.gov/sra-test/slowtests/$(shell whoami)
-
-slowtests: all $(SLOW_TEST_TOOLS)
-	@ export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;\
-	for i in $(SLOW_TEST_TOOLS);\
-	do\
-		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
-		echo Run $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
-		if [ "$$r" != "0" ] ; then exit $$r; fi; \
-	done
+# TODO:
+help:
+	@ echo
+	@ echo "Before initial build, run './configure --build-prefix=<out>' from"
+	@ echo "the project root to set the output directory of your builds and"
+	@ echo "other parameters."
+	@ echo "Run ./configure -h for full description."
+	@ echo
+	@ echo "Make targets:"
+	@ echo " help            : this text"
+	@ echo " config          : print a summary of current configuration"
+	@ echo " all, std        : full build"
+	@ echo " clean           : remove build results, including CMake-generated files"
+	@ echo " test, runtests  : build and run fast tests"
+	@ echo " slowtests       : build and run all (fast and slow) tests"
+	@ echo " install         : build, install to $(INST_LIBDIR)"
+	@ echo
+	@ echo The build uses CMake. CMake-generated files are in $(OBJDIR)
+	@ echo
+	@ echo It is recommended to use 'make -j' for quicker builds.
+	@ echo
 
-.PHONY: slowtests
+.PHONY: help configure
 
 #-------------------------------------------------------------------------------
-# all-cmn
-#
-# Common target to trigger build of all tools
-#
-$(TARGDIR)/all-cmn: $(addprefix $(BINDIR)/,$(ALL_TOOLS))
 
-.PHONY: $(TARGDIR)/all-cmn
+.PHONY: default all std
 
-#-------------------------------------------------------------------------------
-# std-cmn
-#
-# Common target to trigger build of external visibility tools
-#
-$(TARGDIR)/std-cmn: $(addprefix $(BINDIR)/,$(EXT_TOOLS))
 
-.PHONY: $(TARGDIR)/std-cmn
+# TODO: add support for fuzz testing
+FLIBDIR = $(TARGDIR)/fuzz
+
+$(FLIBDIR):
+	mkdir -p $@
+
+fuzz: makedirs
diff --git a/build/Makefile.env.old b/build/Makefile.env.old
new file mode 100644
index 000000000..af853be38
--- /dev/null
+++ b/build/Makefile.env.old
@@ -0,0 +1,424 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+# pick up dependencies from object directory
+ifdef SRCDIR
+	include $(wildcard *.d)
+endif
+
+# determine shell environment
+include $(TOP)/build/Makefile.shell
+
+# load build configuration
+include $(CONFIG_FILE)
+
+# normally build shared and static external libs
+LIBEXT = $(LIBX) $(SHLX)
+
+# normally build static intermediate libs
+ILIBEXT = $(LIBX)
+
+# determine BUILD
+ifeq (,$(BUILD))
+	BUILD = dbg
+endif
+
+# some rules are sensitive to the type of build
+BUILDTYPE = $(BUILD)
+
+# adjust settings for build
+ifeq (dbg,$(BUILD))
+	DEBUG := -D_DEBUGGING
+endif
+ifeq (prof,$(BUILD))
+	DEBUG := -D_PROFILING
+endif
+ifeq (pur,$(BUILD))
+	DEBUG := -D_DEBUGGING
+	LD_PRE := purify
+	LNKG = stat
+endif
+ifeq (pcov,$(BUILD))
+	DEBUG := -D_DEBUGGING
+	LD_PRE := purecov
+	LNKG = stat
+endif
+ifeq (scm,$(BUILD))
+	BUILDTYPE = rel
+	CHECKSUM := --checksum
+endif
+
+ifeq (yes,$(HAS_RHOST))
+	LOCAL_OR_REMOTE = remote
+else
+	LOCAL_OR_REMOTE = local
+endif
+
+# pre-built sra-tools are static
+ifeq (1,$(WANTS_STATIC))
+	STATIC = --static
+	STATICSYSLIBS = --static-system-libs
+endif
+
+# drop all suffix rules
+.SUFFIXES:
+
+# load OS and COMP specific files
+include $(TOP)/build/Makefile.$(OS)
+include $(TOP)/build/Makefile.$(COMP)
+include $(TOP)/build/Makefile.rules
+
+# external schema modules
+EXT_SCHEMA_MODULES = axf sraxf wgsxf vxf
+UPDATE_SCHEMA_LIBS := $(addprefix -lw,$(EXT_SCHEMA_MODULES))
+READONLY_SCHEMA_LIBS = $(addprefix -l,$(EXT_SCHEMA_MODULES))
+ALWAYS_STATIC_SCHEMA_LIBS = $(addprefix -s,$(EXT_SCHEMA_MODULES))
+
+# full directory paths
+TARGDIR ?= $(OUTDIR)/$(OS)/$(TOOLSET)/$(ARCH)/$(BUILD)
+BINDIR ?= $(TARGDIR)/bin
+ifeq (win,$(OS))
+    # on Windows, place test executables next to .dlls
+    TEST_BINDIR = $(BINDIR)
+else
+    TEST_BINDIR = $(TARGDIR)/test-bin
+endif
+ILIBDIR = $(TARGDIR)/ilib
+LIBDIR = $(TARGDIR)/lib
+OBJDIR = $(TARGDIR)/obj/$(MODULE)
+
+CLSPATH         ?= $(TARGDIR)/java
+CLASSPATH       ?= $(CLSPATH)
+CLASSDIR        ?= $(TARGDIR)/$(MODULE)
+TEST_CLSPATH    ?= $(OUTDIR)/test/java
+JAVASOURCEPATH  ?= $(TOP)/java
+
+# path to the ncbi sub-directory
+# this is where modules and installed schema files are kept
+ifeq (win,$(OS))
+    # under Windows, we are always relative to binary path
+	NCBIDIR = $(BINDIR)/ncbi
+else
+	# under Linux and Mac, it can be binary or library
+	NCBIDIR = $(LIBDIR)/ncbi $(BINDIR)/ncbi
+endif
+
+DEFAULT_CRT = $(VDB_SRCDIR)/libs/kfg/certs.kfg
+DEFAULT_KFG = $(VDB_SRCDIR)/libs/kfg/default.kfg
+
+# make reissue command
+MAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
+    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile
+
+JMAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
+    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(CLASSDIR) -f $(SRCDIR)/Makefile
+
+# directory and link creation
+SUBDIRS = bin test-bin ilib lib
+OUTDIRS = schema
+
+# clean rules
+stdclean:
+	@ -rm -rf $(OBJDIR)
+	@ -rm -rf $(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \
+			$(addsuffix .*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
+			$(addsuffix -static.*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
+			$(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS))) \
+			$(addsuffix *,$(addprefix $(TEST_BINDIR)/,$(ALL_TOOLS) $(TEST_TOOLS)))
+
+stdjclean:
+	@ -rm -rf $(CLSPATH) $(CLSDIR)
+
+# removing symbolic links that point to specific builds
+removelinks:
+	@ test ! -h $(OUTDIR)/schema && rm -rf $(OUTDIR)/schema || true
+	@ rm -f $(addprefix $(OUTDIR)/,$(addsuffix $(BITS),$(SUBDIRS)))
+	@ rm -f $(addprefix $(OUTDIR)/,$(OUTDIRS))
+
+$(BINDIR)/ncbi/certs.kfg: $(DEFAULT_CRT)
+	@ mkdir -p $(NCBIDIR)
+	@ cp -v $(DEFAULT_CRT) $@
+
+$(BINDIR)/ncbi/default.kfg: $(DEFAULT_KFG)
+	@ mkdir -p $(NCBIDIR)
+	@ cp -v $(DEFAULT_KFG) $@
+
+# create all required output directories
+makedirs: $(BINDIR)/ncbi/certs.kfg $(BINDIR)/ncbi/default.kfg
+	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
+
+makejdirs:
+	@ mkdir -p $(CLASSDIR) $(CLSDIR)
+
+# build version include files
+vers-includes: makedirs
+	@ $(MAKE_CMD) -s $(TARGDIR)/$@
+
+ifeq (win,$(OS))
+
+# Windows doesn't really support symbolic links
+# we may add them back in when our toolkit is able to create them
+rebuild-dirlinks: makedirs
+	@ true
+else
+
+LNDIRS = $(addprefix ln_,$(SUBDIRS))
+$(LNDIRS):
+	@ ln -s $(TARGDIR)/$(subst ln_,,$@) $(OUTDIR)/$(subst ln_,,$@)$(BITS)
+
+ifdef NOREBUILD_LINKS
+rebuild-dirlinks:
+	@ true
+else
+rebuild-dirlinks: removelinks makedirs $(LNDIRS)
+	@ ln -s $(VDB_INCDIR) $(OUTDIR)/schema
+endif
+
+endif
+
+.PHONY: stdclean removelinks makedirs vers-includes rebuild-dirlinks
+.PHONY: stdjclean makejdirs
+
+# configuration targets
+out:
+	@ echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(BUILD_OS)
+	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
+
+$(RHOSTS):
+	@ cat $(TOP)/rhosts/$@ >> $(TOP)/build/RHOST.$(HOST_OS)
+
+require-proxy-exec:
+	@ $(MAKE) -C $(TOP)/test/proxy_exec proxy-exec
+	@ echo "PROXY_TOOL := $(BINDIR)/proxy-exec" > $(TOP)/build/RHOST.$(HOST_OS)
+
+local:
+	@ rm -f $(TOP)/build/RHOST.$(HOST_OS)
+
+CC:
+	@ echo cc > $(TOP)/build/COMP.$(OS)
+
+GCC:
+	@ echo gcc > $(TOP)/build/COMP.$(OS)
+
+ICC:
+	@ echo icc > $(TOP)/build/COMP.$(OS)
+
+VC++:
+	@ echo vc++ > $(TOP)/build/COMP.$(OS)
+
+CLANG:
+	@ echo clang > $(TOP)/build/COMP.$(OS)
+
+static dynamic:
+	@ echo "there is no longer any difference between static and dynamic builds"
+
+debug:
+	@ echo dbg > $(TOP)/build/BUILD.$(OS)
+
+profile:
+	@ echo prof > $(TOP)/build/BUILD.$(OS)
+
+release:
+	@ echo rel > $(TOP)/build/BUILD.$(OS)
+
+scm:
+	@ echo scm > $(TOP)/build/BUILD.$(OS)
+
+pubtools: release
+
+bindir:
+	@ echo "$(BINDIR)"
+
+targdir:
+	@ echo "$(TARGDIR)"
+
+osdir:
+	@ echo "$(OUTDIR)/$(OS)"
+
+compilers:
+	@ echo "$(COMPILERS)"
+
+architectures:
+	@ echo "$(ARCHITECTURES)"
+
+architecture:
+	@ echo "$(ARCH)"
+
+config:
+	@ echo "  current build is $(LOCAL_OR_REMOTE) $(BUILD_OS) $(BUILD) $(ARCH) build using $(TOOLSET) tools"
+	@ echo "  output target directory is '$(TARGDIR)'"
+	@ echo
+
+purify:
+	@ echo pur > $(TOP)/build/BUILD.$(OS)
+
+purecov:
+	@ echo pcov > $(TOP)/build/BUILD.$(OS)
+
+.PHONY: out CC GCC ICC debug profile release scm purify purecov local local require-proxy-exec $(RHOSTS) bindir report_config
+
+# includes based upon build
+ITF   = $(VDB_INCDIR)/
+OSINC = $(VDB_INCDIR)/os
+CCINC = $(VDB_INCDIR)/cc
+XTINC = $(VDB_INCDIR)/ext
+NGSINC = $(NGS_INCDIR)
+OVERRIDEINC = $(TOP)/interfaces/override
+
+# OS specific source and include dirs
+SRCDIRS_OS = $(SRCDIR)/$(OS)
+INCDIRS_OS = $(OSINC)/$(OS)
+
+# most OS' have a parent type
+ifdef OS_DAD
+
+SRCDIRS_OS += $(SRCDIR)/$(OS_DAD)
+INCDIRS_OS += $(OSINC)/$(OS_DAD)
+
+# some OS' have a grandparent
+ifdef OS_GDAD
+SRCDIRS_OS += $(SRCDIR)/$(OS_GDAD)
+INCDIRS_OS += $(OSINC)/$(OS_GDAD)
+endif
+
+endif
+
+# compiler specific includes
+INCDIRS_COMP = \
+	$(CCINC)/$(COMP)/$(ARCH) \
+	$(CCINC)/$(COMP)
+
+# some compilers have a parent type
+ifdef COMP_DAD
+
+INCDIRS_COMP += \
+	$(CCINC)/$(COMP_DAD)/$(ARCH) \
+	$(CCINC)/$(COMP_DAD)
+
+endif
+
+VPATH = \
+	$(SRCDIR)/$(COMP)/$(ARCH) \
+	$(SRCDIR)/$(COMP) \
+	$(SRCDIRS_OS) \
+	$(SRCDIR)
+
+INCDIRS = \
+	$(addprefix -I,$(OVERRIDEINC)) \
+	$(addprefix -I,$(SRCDIRS_OS)) \
+	$(addprefix -I,$(SRCDIR) $(ITF)) \
+	$(addprefix -I,$(INCDIRS_COMP)) \
+	$(addprefix -I,$(INCDIRS_OS)) \
+	$(addprefix -I,$(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 ?= $(SHLX)
+ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
+
+# default tool parameters
+CFLAGS	= -std=c11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
+CPFLAGS = -std=c++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
+
+#-------------------------------------------------------------------------------
+# runtests
+#
+# MallocScribble=1 is for catching allocation problems on Mac
+#
+HOSTNAME = $(shell hostname)
+WHICHASCP = $(shell which ascp 2> /dev/null)
+HAVE_NCBI_ASCP=1
+ifeq (,${WHICHASCP})
+	HAVE_NCBI_ASCP=
+endif
+ifeq (iebdev21,${HOSTNAME})
+	HAVE_NCBI_ASCP=
+endif
+
+ifeq ($(RUNTESTS_OVERRIDE),)
+runtests: all $(TEST_TOOLS)
+	@ export VDB_CONFIG=$(VDB_CONFIG);export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\
+	for i in $(TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run VDB_CONFIG=$$VDB_CONFIG $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: runtests
+endif
+
+#-------------------------------------------------------------------------------
+# slowtests
+#
+# $(SLOWTESTSDATADIR) should be used to create temporary test files
+SLOWTESTSDATADIR ?= /panfs/pan1.be-md.ncbi.nlm.nih.gov/sra-test/slowtests/$(shell whoami)
+
+slowtests: all $(SLOW_TEST_TOOLS)
+	@ export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;\
+	for i in $(SLOW_TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: slowtests
+
+#-------------------------------------------------------------------------------
+# all-cmn
+#
+# Common target to trigger build of all tools
+#
+$(TARGDIR)/all-cmn: $(addprefix $(BINDIR)/,$(ALL_TOOLS))
+
+.PHONY: $(TARGDIR)/all-cmn
+
+#-------------------------------------------------------------------------------
+# std-cmn
+#
+# Common target to trigger build of external visibility tools
+#
+$(TARGDIR)/std-cmn: $(addprefix $(BINDIR)/,$(EXT_TOOLS))
+
+.PHONY: $(TARGDIR)/std-cmn
diff --git a/build/env.cmake b/build/env.cmake
index a227710d0..e0e7a1f78 100755
--- a/build/env.cmake
+++ b/build/env.cmake
@@ -196,6 +196,10 @@ function(SetAndCreate var path )
     file(MAKE_DIRECTORY ${path} )
 endfunction()
 
+if( NOT TARGDIR )
+    set( TARGDIR ${CMAKE_BINARY_DIR} )
+endif()
+
 if ( ${CMAKE_GENERATOR} MATCHES "Visual Studio.*" OR
      ${CMAKE_GENERATOR} STREQUAL "Xcode" )
     set( SINGLE_CONFIG false )
@@ -213,10 +217,12 @@ if ( ${CMAKE_GENERATOR} MATCHES "Visual Studio.*" OR
     set( NCBI_VDB_ILIBDIR_DEBUG ${VDB_BINDIR}/Debug/ilib )
     set( NCBI_VDB_ILIBDIR_RELEASE ${VDB_BINDIR}/Release/ilib )
 
-    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG   ${CMAKE_BINARY_DIR}/Debug/bin )
-    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_BINARY_DIR}/Release/bin )
-    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG   ${CMAKE_BINARY_DIR}/Debug/lib )
-    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_RELEASE ${CMAKE_BINARY_DIR}/Release/lib )
+    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG   ${TARGDIR}/Debug/bin )
+    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${TARGDIR}/Release/bin )
+    SetAndCreate( TEST_RUNTIME_OUTPUT_DIRECTORY_DEBUG   ${TARGDIR}/Debug/test-bin )
+    SetAndCreate( TEST_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${TARGDIR}/Release/test-bin )
+    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG   ${TARGDIR}/Debug/lib )
+    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_RELEASE ${TARGDIR}/Release/lib )
     set( CMAKE_LIBRARY_OUTPUT_DIRECTORY_DEBUG            ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG} )
     set( CMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE          ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY_RELEASE} )
     set( CMAKE_JAR_OUTPUT_DIRECTORY                      ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG} ) # both Debug and Release share this
@@ -224,6 +230,7 @@ if ( ${CMAKE_GENERATOR} MATCHES "Visual Studio.*" OR
     # to be used in add-test() as the location of executables.
     # NOTE: always use the COMMAND_EXPAND_LISTS option of add_test
     set( BINDIR "$<$<CONFIG:Debug>:${CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG}>$<$<CONFIG:Release>:${CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE}>" )
+    set( TESTBINDIR "$<$<CONFIG:Debug>:${TEST_RUNTIME_OUTPUT_DIRECTORY_DEBUG}>$<$<CONFIG:Release>:${TEST_RUNTIME_OUTPUT_DIRECTORY_RELEASE}>" )
 
     link_directories( $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}> $<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}> )
     link_directories( $<$<CONFIG:Debug>:${NCBI_VDB_ILIBDIR_DEBUG}> $<$<CONFIG:Release>:${NCBI_VDB_ILIBDIR_RELEASE}> )
@@ -239,14 +246,15 @@ else() # assume a single-config generator
     set( NCBI_VDB_LIBDIR ${VDB_BINDIR}/lib )
     set( NCBI_VDB_ILIBDIR ${VDB_BINDIR}/ilib )
 
-    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
-    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib )
+    SetAndCreate( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${TARGDIR}/bin )
+    SetAndCreate( CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${TARGDIR}/lib )
     set( CMAKE_LIBRARY_OUTPUT_DIRECTORY          ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY} )
     set( CMAKE_JAR_OUTPUT_DIRECTORY              ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY} )
 
     # to be used in add-test() as the location of executables.
     # NOTE: always use the COMMAND_EXPAND_LISTS option of add_test
-    set( BINDIR "${CMAKE_BINARY_DIR}/bin" )
+    set( BINDIR "${TARGDIR}/bin" )
+    set( TESTBINDIR "${TARGDIR}/test-bin" )
 
     link_directories( ${NCBI_VDB_LIBDIR} )
     link_directories( ${NCBI_VDB_ILIBDIR} )
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 5a538df4e..685e3a910 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,10 +1,6 @@
-if(NOT CMAKE_TEST_OUTPUT_DIRECTORY)
-    set(CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/test-bin)
-endif()
-
 # this is where test executables will be created
-# to access tools themselves, use ${CMAKE_BINARY_DIR}/bin
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_TEST_OUTPUT_DIRECTORY} )
+# to access tools themselves, use ${BINDIR}
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${TESTBINDIR} )
 
 set( COMMON_LINK_LIBRARIES ${COMMON_LINK_LIBRARIES} ktst )
 link_libraries( ${COMMON_LINK_LIBRARIES} )
diff --git a/test/vcf-loader/CMakeLists.txt b/test/vcf-loader/CMakeLists.txt
index dd5bd79bf..6bb02d77c 100644
--- a/test/vcf-loader/CMakeLists.txt
+++ b/test/vcf-loader/CMakeLists.txt
@@ -5,6 +5,6 @@ if ( NOT WIN32 )
 	target_link_libraries( test-vcf-loader ${COMMON_LINK_LIBRARIES} ncbi-wvdb vcfloader )
 
 	add_test( NAME Test_Vcf_loader
-		COMMAND vcf-loader.sh ${CMAKE_BINARY_DIR}/test-bin/test-vdb-config-model "${VDB_SRCDIR}/interfaces"
+		COMMAND vcf-loader.sh ${TESTBINDIR}/test-vdb-config-model "${VDB_SRCDIR}/interfaces"
 		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
 endif()
\ No newline at end of file
diff --git a/test/vdb-config/CMakeLists.txt b/test/vdb-config/CMakeLists.txt
index e9db7d626..b5a097558 100644
--- a/test/vdb-config/CMakeLists.txt
+++ b/test/vdb-config/CMakeLists.txt
@@ -5,7 +5,7 @@ if ( NOT WIN32 )
 	target_link_libraries( test-vdb-config-model ${COMMON_LINK_LIBRARIES} ncbi-vdb )
 
 	add_test( NAME Test_VDB_Config_model
-		COMMAND model.sh ${CMAKE_BINARY_DIR}/test-bin/test-vdb-config-model
+		COMMAND model.sh ${TESTBINDIR}/test-vdb-config-model
 		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
 
 	add_test( NAME Test_VDB_Config
diff --git a/test/vdb-dump/CMakeLists.txt b/test/vdb-dump/CMakeLists.txt
index 772c5b90a..63f1e6e81 100644
--- a/test/vdb-dump/CMakeLists.txt
+++ b/test/vdb-dump/CMakeLists.txt
@@ -11,6 +11,6 @@ if ( NOT WIN32 )
 	target_link_libraries( vdb-dump-makedb ${COMMON_LINK_LIBRARIES} ncbi-wvdb )
 
 	add_test( NAME Test_Vdb_dump
-		COMMAND vdb_dump.sh "${CMAKE_BINARY_DIR}/test-bin/vdb-dump-makedb" "${BINDIR}"
+		COMMAND vdb_dump.sh "${TESTBINDIR}/vdb-dump-makedb" "${BINDIR}"
 		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
 endif()
\ No newline at end of file
diff --git a/test/vdb-dump/vdb_dump.sh b/test/vdb-dump/vdb_dump.sh
index 7a9b7b6d3..4c40cae06 100755
--- a/test/vdb-dump/vdb_dump.sh
+++ b/test/vdb-dump/vdb_dump.sh
@@ -4,7 +4,6 @@ vdb_dump_makedb=$1
 bin_dir=$2
 
 echo vdb-dump-makedb: ${vdb_dump_makedb}
-echo cmake_source_dir: ${cmake_source_dir}
 
 echo "testing vdb_dump"