.gitignore

-user.status
-vgcore.*
+*~
+.DS_Store
+._*
+*.d
+*.db
+*.o
+*.pyc
 /bin64
+/build/BUILD.*
 /build/COMP.mac
-/build/Makefile.config*
-/build/MSVC/2010/ipch
-/build/MSVC/2010/ncbi-vdb.opensdf
 /centos
 /ilib64
 /lib64
 /mac
-/Makefile.config.mac.arch
+/Makefile.config.*
 /reconfigure
 /schema
 /test-bin64
-user.status
 /win
-*.opensdf
-*.sdf
-*.suo
 *.log
 /.cproject
 /.project
 /.pydevproject
-
-# mac os x meta-files
-.DS_Store
-._*
-
-*~
-\#*
-.\#*
-core
-*.pyc
-.gdb_history
-.vscode
-.gdb_history
+*.stash
+tmp.kfg

LICENSE

@@ -31,18 +31,7 @@ Please cite the authors in any work or product based on this material.
 ==============================================================
 EXCEPTIONS (in all cases excluding NCBI-written makefiles):
 
-Location: {libs,interfaces}/ext/bzip2
-Author:   Julian R Seward
-License:  BSDish [libs/ext/bzip2/LICENSE]
-
-Location: {libs,interfaces}/ext/zlib
-Authors:  Jean-loup Gailly and Mark Adler
-License:  BSDish [interfaces/ext/zlib.h]
-
-Location: libs/klib
-Author:   Douglas C. Schmidt
-License:  GNU Lesser General Public [libs/klib/qsort.c]
-
+See LICENSE from https://github.com/ncbi/ncbi-vdb
 
 ==============================================================
 Copyright F.A.Q.

Makefile

@@ -34,14 +34,15 @@ include $(TOP)/build/Makefile.shell
 # default
 #
 SUBDIRS = \
-	libs \
+	shared \
+	tools \
 
 # common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
 include $(TOP)/build/Makefile.targets
 
 default: $(SUBDIRS)
 
-test: $(SUBDIRS)
+test: all
 
 $(SUBDIRS) test:
 	@ $(MAKE) -C $@
@@ -61,11 +62,10 @@ $(SUBDIRS_STD):
 #-------------------------------------------------------------------------------
 # install
 #
-
 install: 
-	@ echo "Checking make status of object libraries..."
-	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) $(SUBDIRS)
-	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install
+	@ echo "Checking make status of tools..."
+	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) std
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install install
 
 uninstall:    
 	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
@@ -75,7 +75,7 @@ uninstall:
 #-------------------------------------------------------------------------------
 # clean
 #
-clean: clean_test
+clean: clean_deb clean_rpm clean_test
 
 clean_test:
 	@ $(MAKE) -s -C test clean
@@ -88,6 +88,8 @@ runtests: runtests_test
 runtests_test:
 	@ $(MAKE) -s -C test runtests
 
+#	@ $(MAKE) -s -C ngs runtests
+
 #-------------------------------------------------------------------------------
 # slowtests
 #
@@ -104,6 +106,32 @@ 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
 #
@@ -140,7 +168,7 @@ $(REPORTS):
 # configuration help
 #
 help configure:
-	@ echo "Before initial build, run 'make OUTDIR=<dir> out' from"
+	@ 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"

README-blastn

+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+The NCBI SRA ( Sequence Read Archive )
+
+
+Contact: sra-tools@ncbi.nlm.nih.gov
+http://trace.ncbi.nlm.nih.gov/Traces/sra/std
+
+
+Stand-alone BLAST searches against SRA runs in their native format.
+-------------------------------------------------------------------
+
+A stand-alone blastn application to perform BLAST searches directly against 
+native SRA files is included in this distribution. This application has been
+tested in-house at the NCBI, but has not been heavily used, so this should be
+considered a preliminary (alpha) release to a few experienced users. A 64-bit
+LINUX application has been built for this testing. 
+
+The application is called "blastn_vdb".
+
+The application can be invoked in much the same manner as the standard 
+blastn application:
+
+1) blastn_vdb -help or blastn_vdb -h will produce usage messages.
+
+2) The BLAST+ command-line manual at http://www.ncbi.nlm.nih.gov/books/NBK1763/ 
+provides more details on the options, though not all blastn options are
+available with blastn_vdb. Some options simply do not apply to sequences in SRA
+(e.g., -gilist is missing as these sequences have not been assigned GI's). Some
+options have not yet been implemented (e.g., -num_threads is currently disabled).
+
+
+To search cached or on-demand SRA objects.
+------------------------------------------
+An example blastn_vdb command-line would be:
+
+./blastn_vdb -db "ERR039542 ERR047215 ERR039539 ERR039540" -query nt.test -out test.out
+
+The file nt.test contains the query in FASTA format, and it will be searched against 
+the reads in runs with accessions ERR039542 ERR047215 ERR039539 ERR039540.
+
+If you have not already downloaded these objects using the vdb "prefetch" tool,
+they will be retrieved on-demand from NCBI under standard configuration. For
+alternative configuration information, please see the "README-vdb-config" file
+in this distribution.
+
+Searching with manually downloaded files.
+-----------------------------------------
+If you have manually downloaded files, e.g. via aspera or wget, etc., they may
+be referred to as "local" files. You can pass one or more file paths to be used
+collectively as the database. In this case the blastn_vdb command-line would be:
+
+./blastn_vdb -db <SRR_file> -query <input_file> -out <output_file>
+	
+Where
+<SRR_file> is the path (relative or absolute) and name of the SRRxxxxx file
+<input_file> is a fasta file containing the sequence(s) to be BLASTed
+<output_file> is the name specified for the output report of the blast search.
+
+Example:
+
+./blastn_vdb -db ./subdir/ERR039542.sra -query nt.test -out test.out
+
+Querying multiple SRR files simultaneously:
+
+./blastn_vdb -db "<SRR_file1> <SRR_file2> <SRR_file3>" -query <input.fa> -out <output_file>
+
+Enclose the group of files to be included in the search set in "quotes", e.g.
+"./SRR_file1.sra ./SRR_file2.sra ./SRR_file3.sra"
+
+Example:
+
+./blastn_vdb -db "./ERR039542.sra ./ERR047215.sra ./ERR039539.sra ./ERR039540.sra" -query nt.test -out test.out
+
+Caveats
+-------
+There are some limitations on the currently available application:
+
+1) Individual SRA data files containing more than 2 billion reads are not yet supported. For a 
+paired-end experiment this is actually a limitation of about 1 billion "spots".
+
+2) Compressed SRA ("cSRA") is not yet fully supported. Currently, only the
+unaligned fraction of reads are searched. Compressed SRA are runs containing
+alignments (e.g., ERR230455). Runs can be checked with "vdb-dump" to report if
+they contain alignment information:
+
+    $ vdb-dump -E ERR230455
+    enumerating the tables of database 'ERR230455'
+    tbl #1: PRIMARY_ALIGNMENT
+    tbl #2: REFERENCE
+    tbl #3: SEQUENCE
+
+3) You may need to prefix "./" to the run name for files in your current
+directory.
+
+4) The blast_formatter is not currently able to read native SRA files, so 
+reformatting of results saved as a blast archive is not yet supported.
+
+Common errors and fixes.
+------------------------
+
+1) Failure to provide relative path to manually downloaded SRR file:
+
+./blastn_vdb -db SRR770754.sra -query srr770754_test.fa -out test.out
+Error: NCBI C++ Exception:
+    "vdb2blast_util.cpp", line 253: Error: ncbi::CVDBBlastUtil::x_MakeSRASeqSrc() 
+    - VDB BlastSeqSrc construction failed: Failed to add any run to VDB runset: unsupported while allocating
+    
+Fix:
+Include relative (e.g., "../" or "./") or absolute (e.g., "/home/user/SRA_BLAST_data/") file path with SRR file

README-vdb-config

+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+The tool 'vdb-config' can be used to inspect or change the configuration
+of the sra-toolkit.
+
+When called without any parameters the tool reports the current configuration
+in xml-format. No changes are made.
+
+-----------------------------------------------------------------------------
+
+vdb-config --restore-defaults
+
+If called with this parameter the tool will bring the configuration into
+default state.
+
+-----------------------------------------------------------------------------
+
+vdb-config -i
+
+This will present the user with a colored configuration dialog.
+
+The tab-key and the cursor-keys navigate the dialog. The item with the little
+red square has the focus. A button or a checkbox can be 'pressed' with the
+space or enter-key. To get out of the dialog without saving any changes
+press the '6'-key or the 'q'-key or navigate to the 'exit'-button at the
+bottom of the dialog and press the space or enter-key.
+
+
+The "data source" part:
+
+The "NCBI SRA" labeled checkbox enables/disables remote access to the SRA-
+accession stored at NCBI. As long as the computer has internet-access and this
+checkbox is enabled the user can access SRA-accessions directly without
+downloading them.
+
+A command like 'sra-pileup SRR341578' at the command-line will produce pileup
+output of the given accession even if this accession has not been downloaded
+before.
+The tool will download the data on the fly from our servers.
+
+
+There might be a checkbox labeled "site" below the "NCBI-SRA" one. If this
+checkbox is not available you do not have a 'site'-installation of SRA-data.
+If it is visible you do have such a site-installation and you can disable
+access to this data.
+
+
+The "local workspaces" part:
+
+At the top are 2 buttons "import dbGaP-project" and "set default import path".
+
+If you are not using dbGaP-projects (The database of Genotypes and Phenotypes)
+you can ignore these 2 buttons.
+
+The "import dbGaP-project" button presents you with another dialog to select
+a ngc-file. You can navigate the directories of your computer to find and
+select one of these files. By default the focus is in the files-list. It may
+be empty.
+Use the cursor-key: 'up' to focus the 'directories'-list. If you press enter
+on any of the listed directory-names you change into this directory.
+The '[ .. ]' entry brings you back into the parent directory. If you see
+ngc-files in the lower 'files'-list press the tab-key to switch to the
+'files'-list. Press enter on one of them to select this file for import. You
+will see a success-message if the import was performed without errors.
+On Windows you cannot switch from one drive-letter
+to another when selecting.
+
+The "set default import path" gives you the opportunity to specify a different
+default location for dbGaP-projects - for instance if your home directory is
+not big enough. You can always change the location for your dbGaP-project
+after the import.
+
+
+Below the 2 buttons is a list of local repositories. If there are no
+dbGaP-projects this list has only one entry "Open Access Data". This is the
+location where accessions get downloaded and cached. You can change these
+locations if for instance your home directory where they are created by
+default does not have enough space.
+The change button brings up a directory-select dialog.
+
+If you made any changes like enabling/disabling or changed a location, the
+change is only written to the configuration if you exit the dialog via the
+'save and exit' button.
+
+-----------------------------------------------------------------------------
+
+
+vdb-config -i --interactive-mode textual
+
+This will present the user with a purely textual and sequential dialog. It is
+intended to be used if the colored mode does not work, maybe because of
+console issues.

README.md

@@ -2,14 +2,25 @@
 
 ### Contact:
 email: sra-tools@ncbi.nlm.nih.gov
+or visit the [SRA Tools web site](http://ncbi.github.io/sra-tools)
+
+### Download
+Visit our [download page](https://github.com/ncbi/sra-tools/wiki/Downloads) for pre-built binaries.
 
 ### Change Log
 Please check the CHANGES.md file for change history.
 
-## NCBI VDB
+## The SRA Toolkit
 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
 using data in the INSDC Sequence Read Archives.
 
+### ANNOUNCEMENT:
+With release 2.9.1 of `sra-tools` we have finally made available the tool `fasterq-dump`, a replacement for the much older `fastq-dump` tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files. `fasterq-dump` is multi-threaded and performs bulk joins in a way that improves performance as compared to `fastq-dump`, which performs joins on a per-record basis _(and is single-threaded)_.
+
+`fastq-dump` is still supported as it handles more corner cases than `fasterq-dump`, but it is likely to be deprecated in the future.
+
+You can get more information about `fasterq-dump` in our Wiki at [https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump).
+
 ### IMPORTANT ANNOUNCEMENT
 As was announced in [OMB memorandum M-15-13](https://www.whitehouse.gov/sites/default/files/omb/memoranda/2015/m-15-13.pdf) on June 8, 2015, NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as `sra-tools`, `ncbi-vdb` or `ngs`.
 

build/.gitignore

 .cvsignore
-RHOST* ARCH* BUILD* COMP* OUTDIR*
+RHOST* ARCH* COMP* OUTDIR*
 STATIC
 ld.linux.exe_cmd.sh
 LNKG.*
-*.sdf
-*.suo
-*.user
-
-
+Makefile.config*

build/Makefile.clang

@@ -36,18 +36,21 @@ PP = gcc -E $(CFLAGS)
 LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
 
 LPFLAGS = $(LDFLAGS)
 
 LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \
-	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
+	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
 
 # tool options
 WARN = -Wall -Wno-variadic-macros -Wno-long-long # -Wconversion
-# TODO: Lots of new clang options in later versions (-fsanitize, CFI, CPI, ...)
+ifeq (linux,$(OS))
+    NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
+endif
+
 ifeq (64,$(BITS))
 	CARCH = -m64
 else    

build/Makefile.deb

+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+#VERBOSE=-v
+
+# determine shell environment ($CONFIG_FILE)
+include $(TOP)/build/Makefile.shell
+
+# load build configuration ($TARGDIR) ($VERSION)
+include $(CONFIG_FILE)
+
+# $TOOLS_TO_INSTALL
+include $(TOP)/build/Makefile.tools
+ifeq (1,$(HAVE_HDF5))
+	TOOLS_TO_INSTALL += pacbio-load
+endif
+
+PKGDIR=$(TARGDIR)/debbuild
+DST=$(PKGDIR)/sra-toolkit-$(VERSION)
+DEB=$(DST).deb
+
+TOOL=$(shell which dpkg-deb 2> /dev/null)
+
+################################################################################
+
+clean_deb:
+	rm -rf $(DEB) $(DST)
+
+ifeq ("","$(TOOL)")
+deb:
+	>&2 echo dpkg-deb: command not found
+else
+deb: $(DEB)
+endif
+
+DEB_DEPS =                       \
+	$(DST)/etc/ncbi/default.kfg  \
+	$(DST)/etc/ncbi/certs.kfg    \
+	$(DST)/etc/ncbi/schema.kfg   \
+	$(DST)/etc/ncbi/vdb-copy.kfg \
+	$(DST)/usr/bin               \
+	$(DST)/DEBIAN/control
+
+$(DEB): $(DEB_DEPS)
+ifeq (mac,$(OS))
+	         dpkg-deb --build $(DST)
+else
+	fakeroot dpkg-deb --build $(DST)
+endif
+
+$(PKGDIR):
+	mkdir $(VERBOSE) -p $@
+
+$(DST): $(PKGDIR)
+	mkdir $(VERBOSE) -p $@/DEBIAN
+	mkdir $(VERBOSE) -p $@/etc/ncbi
+
+$(DST)/etc/ncbi:
+	mkdir -p $@
+
+$(DST)/etc/ncbi/default.kfg: $(DST)/etc/ncbi
+	rsync $(VERBOSE) -l --chmod=g-w $(VDB_LIBDIR)/ncbi/default.kfg $@
+
+$(DST)/etc/ncbi/certs.kfg: $(DST)/etc/ncbi
+	rsync $(VERBOSE) -l --chmod=g-w $(VDB_LIBDIR)/ncbi/certs.kfg $@
+
+$(DST)/etc/ncbi/schema.kfg: $(DST)/etc/ncbi
+	echo '/vdb/schema/paths = "/usr/share/ncbi/schema"' > $@
+
+$(DST)/etc/ncbi/vdb-copy.kfg: $(DST)/etc/ncbi
+	rsync $(VERBOSE) -l --chmod=g-w $(BINDIR)/ncbi/vdb-copy.kfg $@
+
+$(DST)/usr/bin: $(DST)
+	mkdir $(VERBOSE) -p $@
+	$(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.deb \
+		$(TOOLS_TO_INSTALL)
+
+$(DST)/usr/share/ncbi/schema: $(DST)
+	mkdir $(VERBOSE) -p $@
+	rsync $(VERBOSE) -rmloptD --include '*.vschema' --include='*/' \
+		 --exclude '*' $(VDB_INCDIR)/* $@
+
+$(DST)/DEBIAN/control:
+	mkdir $(VERBOSE) -p $(DST)/DEBIAN
+	printf \
+"Package: sra-toolkit\n"\
+"Version: $(VERSION)\n"\
+"Architecture: all\n"\
+"Maintainer: SRA Toolkit Development Team <sra-tools@ncbi.nlm.nih.gov>\n"\
+"Description: SRA Toolkit package\n"\
+" The SRA Toolkit and SDK from NCBI is a collection of tools and libraries\n"\
+" for using data in the INSDC Sequence Read Archives.\n" > $@
+
+$(TOOLS_TO_INSTALL):
+	- ( test -f $(BINDIR)/$@ || ( echo "$@ not found" && false ) ) && \
+		rsync $(VERBOSE) -l $(BINDIR)/$@ $(BINDIR)/$@$(VERSION_EXEX) \
+			$(BINDIR)/$@$(MAJVERS_EXEX) $(DST)/usr/bin

build/Makefile.env

@@ -75,6 +75,11 @@ 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:
@@ -119,6 +124,9 @@ else
 	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
@@ -130,21 +138,14 @@ JMAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG)
 SUBDIRS = bin test-bin ilib lib
 OUTDIRS = schema
 
-# compilation rules
-MAKE_JOBS = 1
-
-stdcompile: makedirs
-	@ $(MAKE_CMD) -j$(MAKE_JOBS) $(TARGDIR)/compile
-
 # clean rules
 stdclean:
 	@ -rm -rf $(OBJDIR)
-	@ -rm -rf $(addprefix $(OUTDIR)/$(OS)/$(TOOLSET)/,dyn stat)
 	@ -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) $(SLOW_TEST_TOOLS)))
+			$(addsuffix *,$(addprefix $(TEST_BINDIR)/,$(ALL_TOOLS) $(TEST_TOOLS)))
 
 stdjclean:
 	@ -rm -rf $(CLSPATH)
@@ -155,11 +156,19 @@ removelinks:
 	@ 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:
+makedirs: $(BINDIR)/ncbi/certs.kfg $(BINDIR)/ncbi/default.kfg
 	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
 
-makejdirs: makedirs
+makejdirs:
 	@ mkdir -p $(CLASSDIR)
 
 # build version include files
@@ -183,12 +192,12 @@ rebuild-dirlinks:
 	@ true
 else
 rebuild-dirlinks: removelinks makedirs $(LNDIRS)
-	@ ln -s $(TOP)/interfaces $(OUTDIR)/schema
+	@ ln -s $(VDB_INCDIR) $(OUTDIR)/schema
 endif
 
 endif
 
-.PHONY: compile stdcompile stdclean removelinks makedirs vers-includes rebuild-dirlinks
+.PHONY: stdclean removelinks makedirs vers-includes rebuild-dirlinks
 .PHONY: stdjclean makejdirs
 
 # configuration targets
@@ -270,10 +279,10 @@ purecov:
 .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 = $(TOP)/interfaces
-OSINC = $(TOP)/interfaces/os
-CCINC = $(TOP)/interfaces/cc
-XTINC = $(TOP)/interfaces/ext
+ITF   = $(VDB_INCDIR)/
+OSINC = $(VDB_INCDIR)/os
+CCINC = $(VDB_INCDIR)/cc
+XTINC = $(VDB_INCDIR)/ext
 NGSINC = $(NGS_INCDIR)
 OVERRIDEINC = $(TOP)/interfaces/override
 
@@ -325,15 +334,31 @@ INCDIRS = \
 	-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=gnu11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-CPFLAGS = -std=gnu++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-# some LDFLAGS may have been specified in $(CONFIG_FILE)
-LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)
+CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
+CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
 
 #-------------------------------------------------------------------------------
 # runtests
@@ -342,8 +367,7 @@ LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)
 #
 ifeq ($(RUNTESTS_OVERRIDE),)
 runtests: all $(TEST_TOOLS)
-	@ export VDB_CONFIG=$(VDB_CONFIG);\
-	export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\
+	@ export VDB_CONFIG=$(VDB_CONFIG);export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\
 	for i in $(TEST_TOOLS);\
 	do\
 		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
@@ -371,3 +395,20 @@ slowtests: all $(SLOW_TEST_TOOLS)
 
 .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

build/Makefile.gcc

@@ -36,14 +36,14 @@ PP = gcc -E $(CFLAGS)
 LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
 
 LPFLAGS = $(LDFLAGS)
 
 LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
 	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
 
 # tool options
 WARN = -Wall -Wno-long-long 
@@ -51,6 +51,10 @@ ifneq (sun,$(OS))
     WARN += -Wno-variadic-macros
 endif
 
+ifeq (linux,$(OS))
+    NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
+endif
+
 ifeq (64,$(BITS))
 	CARCH = -m64
 else
@@ -67,15 +71,19 @@ endif
 
 ifeq (dbg, $(BUILD))
 	DBG = -g
-	OPT = $(WARN) -Wno-variadic-macros -fno-strict-aliasing -fstack-protector -Wa,--noexecstack -Wall
-	NOPT = $(WARN) -Wno-variadic-macros -fno-strict-aliasing -fstack-protector -Wa,--noexecstack -Wall
+	OPT = $(WARN)
+	NOPT = $(WARN)
 	# GCC seems unable to use c99 without ansi, which
 	# basically clobbers features back to c89. the options
 	# must be specified in the order shown.
-	PED = -std=gnu11 -pedantic # -fdiagnostics-show-option
+	PED = -std=gnu99 -pedantic # -fdiagnostics-show-option
 else
-	# TODO: use -fstack-protector-strong for gcc >= 4.9
-	OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -fstack-protector -Wa,--noexecstack -Wall -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-c++11-extensions
+
+OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1
+ifeq (x86_64, $(ARCH))
+	OPT += -Wall
+endif
+
 endif
 
 ifeq (mac,$(OS))

build/Makefile.install

@@ -28,15 +28,25 @@ include $(TOP)/build/Makefile.shell
 # load build configuration
 include $(CONFIG_FILE)
 
+# load platform-specific settings
+include $(TOP)/build/Makefile.$(OS)
+
 #-------------------------------------------------------------------------------
-# set up installation locations
+# install
+#
+
+# $TOOLS_TO_INSTALL
+include $(TOP)/build/Makefile.tools
+ifeq (1,$(HAVE_HDF5))
+        TOOLS_TO_INSTALL += pacbio-load
+endif
 
 # unset outside defined variables
 ROOT =
 LINUX_ROOT =
 
 #fake root for debugging
-#uncomment this line and change the following test for root ( see under install: ) to succeed:
+#uncomment this line and change the test for root ( see under install: ) to succeed:
 #ROOT = ~/root
 ifeq (linux, $(OS))
     ifeq (0, $(shell id -u))
@@ -46,93 +56,71 @@ endif
 
 ifeq (true, $(LINUX_ROOT))
     KONFIG_DIR = $(ROOT)/etc/ncbi
-    INCLUDE_SYMLINK = $(ROOT)/usr/include/ncbi-vdb
     PROFILE_FILE = $(ROOT)/etc/profile.d/ncbi-vdb
 else
-    KONFIG_DIR = $(LIB_TARGET)/ncbi
+    KONFIG_DIR = $(INST_BINDIR)/ncbi
 endif
 
-#-------------------------------------------------------------------------------
-# install
-#
-LIBRARIES_TO_INSTALL = \
-    ncbi-vdb.$(VERSION_LIBX) \
-    ncbi-vdb.$(VERSION_SHLX) \
-    ncbi-wvdb.$(VERSION_LIBX) \
-    ncbi-wvdb.$(VERSION_SHLX) \
-    ncbi-ngs-c++.$(VERSION_LIBX) \
-
-LIB_TARGET = $(INST_LIBDIR)$(BITS)
+EXE_TARGET = $(INST_BINDIR)
+PROFILE_FILE = $(ROOT)/etc/profile.d/sra-tools
 
-LIBRARIES_WITH_PREFIX = \
-	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
+installexes:
+	@ echo "Installing executables to $(INST_BINDIR)/..."
+	@ mkdir -p $(INST_BINDIR)
+	@ $(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.install $(TOOLS_TO_INSTALL)
+	@ printf "Installing magic file..."
+	@ $(COPY) $(TOP)/tools/copycat/magic $(INST_BINDIR) && echo "done"
 
-checkversion:
+$(TOOLS_TO_INSTALL):
+	@ printf "Installing $@..."
+	@ # ignore missing tools
+	@ - ( test -f $(BINDIR)/$@$(EXEX) || ( echo "not found" && false ) ) && \
+      $(COPY) $(BINDIR)/$@$(EXEX) $(BINDIR)/$@$(VERSION_EXEX) $(BINDIR)/$@$(MAJVERS_EXEX) $(INST_BINDIR) && \
+      echo "done"
 
-copylibs: checkversion $(LIB_TARGET)
-	@ echo "Installing libraries to $(LIB_TARGET)"
-	@ $(MAKE) -f $(TOP)/build/Makefile.install $(LIBRARIES_WITH_PREFIX)
-
-copyincludes: checkversion
-	@echo "Installing includes to $(INST_INCDIR)"
-	@mkdir -p $(INST_INCDIR)/ncbi-vdb
-	@cp $(TOP)/interfaces/ngs/ncbi/NGS.hpp $(INST_INCDIR)/ncbi-vdb
-
-copykfg: checkversion
+copykfg:
 	@ echo "Installing configuration files to $(KONFIG_DIR)"
-	@ $(TOP)/build/install-kfg.sh default.kfg $(TOP)/libs/kfg $(KONFIG_DIR) $(TOP)/libs/kfg/kfgsums
-	@ $(TOP)/build/install-kfg.sh certs.kfg   $(TOP)/libs/kfg $(KONFIG_DIR) $(TOP)/libs/kfg/kfgsums
+	@ $(TOP)/build/install-kfg.sh default.kfg   $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums
+	@ $(TOP)/build/install-kfg.sh certs.kfg     $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums
+	@ $(TOP)/build/install-kfg.sh vdb-copy.kfg  $(TOP)/tools/vdb-copy   $(KONFIG_DIR) $(TOP)/shared/kfgsums
 	@ # rename obsolete ncbi-vdb.kfg
 	@ if [ -f $(KONFIG_DIR)/ncbi-vdb.kfg ] ; \
         then mv -v $(KONFIG_DIR)/ncbi-vdb.kfg  $(KONFIG_DIR)/ncbi-vdb.kfg.orig  ; fi
 
-install: copylibs copyincludes copykfg
+install: installexes copykfg
 ifeq (true, $(LINUX_ROOT))
-	@ # install symlink to includes
-	@ echo "Updating $(INCLUDE_SYMLINK)"
-	@ rm -f $(INCLUDE_SYMLINK)
-	@ ln -s $(INST_INCDIR)/ncbi-vdb $(INCLUDE_SYMLINK)
 	@ echo "Updating $(PROFILE_FILE).[c]sh"
 	@ printf \
 "#version $(VERSION)\n"\
-"if ! echo \$$LD_LIBRARY_PATH | /bin/grep -q $(LIB_TARGET)\n"\
-"then export LD_LIBRARY_PATH=$(LIB_TARGET):\$$LD_LIBRARY_PATH\n"\
-"fi\n" \
-"export NCBI_VDB_LIBDIR=$(LIB_TARGET)\n" \
+"if ! echo \$$PATH | /bin/grep -q $(EXE_TARGET)\n"\
+"then export PATH=$(EXE_TARGET):\$$PATH\n"\
+"fi" \
         >$(PROFILE_FILE).sh && chmod 644 $(PROFILE_FILE).sh || true;
 	@ printf \
 "#version $(VERSION)\n"\
-"echo \$$LD_LIBRARY_PATH | /bin/grep -q $(LIB_TARGET)\n"\
-"if ( \$$status ) setenv LD_LIBRARY_PATH $(LIB_TARGET):\$$LD_LIBRARY_PATH\n"\
-"setenv NCBI_VDB_LIBDIR $(LIB_TARGET)\n" \
+"echo \$$PATH | /bin/grep -q $(EXE_TARGET)\n"\
+"if ( \$$status ) setenv PATH $(EXE_TARGET):\$$PATH\n"\
         >$(PROFILE_FILE).csh && chmod 644 $(PROFILE_FILE).csh || true;
 	@ #TODO: check version of the files above
-	@ #
-	@ echo "Use \$$NCBI_VDB_LIBDIR in your link commands, e.g.:"
-	@ echo "      ld -L\$$NCBI_VDB_LIBDIR -lncbi-vdb ..."
-	@ #
-	@ echo "Please add $(LIB_TARGET) to your LD_LIBRARY_PATH, e.g.:"
-	@ echo "      export LD_LIBRARY_PATH=$(LIB_TARGET):\$$LD_LIBRARY_PATH"
-	@ #
-	@ echo "Use $(LIB_TARGET) in your link commands, e.g.:"
-	@ echo "      export NCBI_VDB_LIBDIR=$(LIB_TARGET)"
-	@ echo "      ld -L\$$NCBI_VDB_LIBDIR -lncbi-vdb ..."
 endif
 
 #-------------------------------------------------------------------------------
 # uninstall
 #
 
-TO_UNINSTALL = $(LIB_TARGET)/libncbi-vdb* $(LIB_TARGET)/libncbi-wvdb* $(LIB_TARGET)/libncbi-ngs-c++* $(INST_INCDIR)/ncbi-vdb $(KONFIG_DIR)/*.kfg
-TO_UNINSTALL_AS_ROOT = $(INCLUDE_SYMLINK) $(PROFILE_FILE).sh $(PROFILE_FILE).csh
+TO_UNINSTALL = $(addsuffix *,$(addprefix $(INST_BINDIR)/,$(TOOLS_TO_INSTALL) magic))
+ifneq (true, $(LINUX_ROOT))
+    TO_UNINSTALL += $(INST_BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi/ncbi-vdb.kfg $(INST_BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi/vdb-copy.kfg
+endif
+TO_UNINSTALL_AS_ROOT = $(ROOT)/etc/ncbi/certs.kfg $(ROOT)/etc/ncbi/default.kfg $(ROOT)/etc/ncbi/vdb-copy.kfg $(PROFILE_FILE).sh $(PROFILE_FILE).csh
 
 uninstall:
-	@ echo "Uninstalling $(TO_UNINSTALL) ..."
-	@ rm -rf $(TO_UNINSTALL)
+	@ echo "Uninstalling sra-tools from $(INST_BINDIR)..."
+	rm -rf $(TO_UNINSTALL)
 ifeq (true, $(LINUX_ROOT))
 	@ echo "Uninstalling $(TO_UNINSTALL_AS_ROOT) ..."
 	@ rm -rf $(TO_UNINSTALL_AS_ROOT)
 endif
 	@ echo "done."
 
-.PHONY: install copylibs copyincludes checkversion uninstall
+.PHONY: install installexes uninstall

build/Makefile.linux

@@ -70,8 +70,11 @@ LEX = @ true
 # build matrix
 COMPILERS = GCC # ICC
 
+# copy without following symlinks
+COPY = cp -P
+
 # valgrind
-VALGRIND = export NCBI_VALGRIND=ncbi; valgrind --error-exitcode=1 --suppressions=$(TOP)/build/valgrind.suppress --show-reachable=no --quiet --leak-check=full
+VALGRIND = export NCBI_VALGRIND=ncbi; valgrind --error-exitcode=1 --suppressions=$(TOP)/build/valgrind.suppress --show-reachable=no 
 
 VALGRIND_TARGETS = $(addprefix vg-,$(TEST_TOOLS))
 

build/Makefile.rpm

+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+#VERBOSE=-v
+
+# determine shell environment ($CONFIG_FILE)
+include $(TOP)/build/Makefile.shell
+
+# load build configuration ($TARGDIR) ($VERSION)
+include $(CONFIG_FILE)
+
+# $TOOLS_TO_INSTALL
+include $(TOP)/build/Makefile.tools
+ifeq (1,$(HAVE_HDF5))
+	TOOLS_TO_INSTALL += pacbio-load
+endif
+
+REVISION=0
+PKGDIR=$(TARGDIR)/rpmbuild
+RPM =$(PKGDIR)/RPMS/$(ARCH)/sra-toolkit-$(VERSION)-$(REVISION).$(ARCH).rpm
+SRC =$(PKGDIR)/SOURCES/sra-toolkit-$(VERSION).tar.gz
+SPEC=$(PKGDIR)/SPECS/sra-toolkit.spec
+DST =$(PKGDIR)/sra-toolkit-$(VERSION)
+TGZ=$(DST).tar.gz
+
+clean_rpm:
+	echo 'DEBUGGING RPM: clean_rpm'
+	rm -rf $(DST) $(RPM) $(SPEC) $(SRC) $(TGZ)
+
+rpm: $(RPM)
+#	echo DEBUGGING RPM: rpm $(TOP)/$(MODULE)
+
+$(RPM): $(SPEC) $(SRC)
+#	echo 'DEBUGGING RPM: (RPM)'
+	rpmbuild --define "_topdir $(PKGDIR)"  --define "_tmppath %{_topdir}/tmp" \
+	    -bb $(SPEC)
+
+SRC_DEPS =                       \
+	$(DST)/etc/ncbi/default.kfg  \
+	$(DST)/etc/ncbi/certs.kfg    \
+	$(DST)/etc/ncbi/schema.kfg   \
+	$(DST)/etc/ncbi/vdb-copy.kfg \
+	$(DST)/usr/share/ncbi/schema
+
+$(SRC): $(SRC_DEPS)
+	echo 'DEBUGGING RPM: (SRC)'
+	chmod -R g-w $(DST)
+	cd $(PKGDIR) ; tar $(VERBOSE) -zcf $(TGZ) --owner 0 --group 0 \
+		sra-toolkit-$(VERSION)
+	mkdir $(VERBOSE) -p $(PKGDIR)/SOURCES
+	cp $(VERBOSE) -p $(TGZ) $@
+
+$(DST)/etc/ncbi/default.kfg: $(DST)
+	echo 'DEBUGGING RPM: (/etc/ncbi/default.kfg)'
+	rsync $(VERBOSE) -l --chmod=g-w $(VDB_LIBDIR)/ncbi/default.kfg $@
+
+$(DST)/etc/ncbi/certs.kfg: $(DST)
+	echo 'DEBUGGING RPM: (/etc/ncbi/certs.kfg)'
+	rsync $(VERBOSE) -l --chmod=g-w $(VDB_LIBDIR)/ncbi/certs.kfg $@
+
+$(DST)/etc/ncbi/schema.kfg: $(DST)
+	echo 'DEBUGGING RPM: (/etc/ncbi/schema.kfg)'
+	echo '/vdb/schema/paths = "/usr/share/ncbi/schema"' > $@
+
+$(DST)/etc/ncbi/vdb-copy.kfg: $(DST)
+	echo 'DEBUGGING RPM: (/etc/ncbi/vdb-copy.kfg)'
+	rsync $(VERBOSE) -l --chmod=g-w $(BINDIR)/ncbi/vdb-copy.kfg $@
+
+$(DST): $(PKGDIR)
+#	echo 'DEBUGGING RPM: (DST)'
+	mkdir $(VERBOSE) -p $(DST)/etc/ncbi
+	mkdir $(VERBOSE) -p $(DST)/usr/bin
+	$(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.rpm \
+		$(TOOLS_TO_INSTALL)
+
+$(DST)/usr/share/ncbi/schema: $(DST)
+	echo 'DEBUGGING RPM: (/usr/share/ncbi/schema)'
+	mkdir $(VERBOSE) -p $@
+	rsync $(VERBOSE) -rmloptD --include '*.vschema' --include='*/' \
+		 --exclude '*' $(VDB_INCDIR)/* $@
+
+$(PKGDIR):
+	echo 'DEBUGGING RPM: (PKGDIR)'
+	mkdir $(VERBOSE) -p $@/{RPMS,SRPMS,BUILD,SOURCES,SPECS,tmp}
+
+$(TOOLS_TO_INSTALL):
+#	echo 'DEBUGGING RPM: (TOOLS_TO_INSTALL)'
+	- ( test -f $(BINDIR)/$@ || ( echo "$@ not found" && false ) ) && \
+		rsync $(VERBOSE) -l $(BINDIR)/$@ $(BINDIR)/$@$(VERSION_EXEX) \
+			$(BINDIR)/$@$(MAJVERS_EXEX) $(DST)/usr/bin
+
+$(SPEC): $(PKGDIR) $(TOP)/build/Makefile.rpm
+#	echo 'DEBUGGING RPM: (SPEC)'
+	mkdir -p $(PKGDIR)/SPECS
+	printf \
+"%%define        __spec_install_post %%{nil}\n"\
+"%%define          debug_package     %%{nil}\n"\
+"%%define        __os_install_post   %%{_dbpath}/brp-compress\n"\
+"\n"\
+"Summary: SRA Toolkit package\n"\
+"Name: sra-toolkit\n"\
+"Version: $(VERSION)\n"\
+"Release: $(REVISION)\n"\
+"License: Public Domain\n"\
+"Group: NCBI/VDB\n"\
+"SOURCE0 : %%{name}-%%{version}.tar.gz\n"\
+"URL: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software\n"\
+"\n"\
+"BuildRoot: %%{_tmppath}/%%{name}-%%{version}-%%{release}-root\n"\
+"\n"\
+"%%description\n"\
+"%%{summary}\n"\
+"\n"\
+"%%prep\n"\
+"%%setup -q\n"\
+"\n"\
+"%%build\n"\
+"# Empty section.\n"\
+"\n"\
+"%%install\n"\
+"rm   -rf %%{buildroot}\n"\
+"mkdir -p %%{buildroot}\n"\
+"\n"\
+"# in builddir\n"\
+"cp -a * %%{buildroot}\n"\
+"\n"\
+"%%clean\n"\
+"rm -rf %%{buildroot}\n"\
+"\n"\
+"%%files\n"\
+"%%defattr(-,root,root,-)\n"\
+"%%{_bindir}/*\n"\
+"/etc/ncbi/*\n"\
+"/usr/share/ncbi/schema/*/*\n"\
+"\n"\
+"%%post\n"\
+"if [ -e /etc/profile.d/sra-tools.csh ] || [ -e /etc/profile.d/sra-tools.sh  ]"\
+"\n"\
+"then\n"\
+"    FOUND=1\n"\
+"fi\n"\
+'if [ "$$FOUND" != "" ] ; then'\
+"\n"\
+"    echo User installation of sra-tools is found.\n"\
+"    if [ -e /etc/profile.d/sra-tools.csh ] ; then\n"\
+"        mv -v /etc/profile.d/sra-tools.csh /etc/profile.d/sra-tools.csh.bak\n"\
+"    fi\n"\
+"    if [ -e /etc/profile.d/sra-tools.sh ] ; then\n"\
+"        mv -v /etc/profile.d/sra-tools.sh /etc/profile.d/sra-tools.sh.bak\n"\
+"    fi\n"\
+"    echo /etc/profile.d/sra-tools.[c]sh was updated.\n"\
+"    echo You might need to relogin to have your PATH variable updated.\n"\
+"fi\n" > $@

build/Makefile.rules

@@ -100,10 +100,9 @@ LOC_INFO = -D__mod_name__=$(MODULE) -D__file_name__=$*
 	$(CP) -S -o $@ -fPIC $(NOPT) $<
 
 # yacc and lex
-# these are disabled for now (and LEX and YACC defined as 'true') - use source controlled .c files;
-#$(SRCDIR)/%.c: %.y
+#%.c: %.y
 #	$(YACC) -o $@ $^
-#$(SRCDIR)/%.c: %.l
+#%.c: %.l
 #	$(LEX) -DYY_BUF_SIZE=16777216 -t $< | grep -v '^#line' > $@
 
 # version include generation

build/Makefile.shell

@@ -24,7 +24,7 @@
 
 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")
+    $(error "*** File '$(CONFIG_FILE)' is missing. Please run $(TOP)/configure")
 endif
 
 # determine OS
@@ -35,6 +35,11 @@ ifeq (Darwin, $(UNAME))
 endif
 ifeq (Linux, $(UNAME))
 	HOST_OS = linux
+	OS_DISTRIBUTOR = $(shell lsb_release -si)
+	EXECMDF = $(TOP)/build/ld.linux.exe_cmd.sh
+	ifeq (no, $(shell test -f $(EXECMDF) && echo yes || echo no))
+        	$(error "*** File '$(EXECMDF)' is missing. Please run $(TOP)/configure")
+	endif
 endif
 ifeq (SunOS, $(UNAME))
 	HOST_OS = sun
@@ -55,6 +60,14 @@ BUILD_OS = $(OS)
 ARCHITECTURES = default
 ifeq (mac,$(HOST_OS))
 	HOST_ARCH = $(shell $(TOP)/build/mac.arch.sh)
+	OS_ARCH = $(shell perl $(TOP)/setup/os-arch.perl)
+	CONFIG_FILE_OA = $(TOP)/build/Makefile.config.$(OS_ARCH)
+	ifeq (no, $(shell test -f $(CONFIG_FILE_OA) && echo yes || echo no))
+    	$(error "*** File '$(CONFIG_FILE_OA)' is missing. Please run $(TOP)/configure")
+	endif
+	ifeq (no, $(shell grep CONFIGURE_FOUND_XML2 $(CONFIG_FILE_OA) && echo yes || echo no))
+    	$(error "*** 'CONFIGURE_FOUND_XML2' is missing in $(CONFIG_FILE_OA). Please run $(TOP)/configure")
+	endif
 else
 	MARCH = $(shell uname -m)
 

build/Makefile.targets

@@ -103,7 +103,6 @@ $(SUBDIRS_SLOWTESTS):
 
 .PHONY: slowtests $(SUBDIRS_SLOWTESTS)
 
-
 #-------------------------------------------------------------------------------
 # valgrind
 #
@@ -115,3 +114,4 @@ $(SUBDIRS_VALGRIND):
 	@ $(MAKE) -C $(subst _valgrind,,$@) valgrind
 
 .PHONY: valgrind $(SUBDIRS_VALGRIND)
+

build/Makefile.tools

+TOOLS_TO_INSTALL = \
+	abi-dump        \
+	abi-load        \
+	align-info      \
+	bam-load        \
+	cache-mgr       \
+	cg-load         \
+	copycat         \
+	fasterq-dump    \
+	fastq-dump      \
+	fastq-load      \
+	helicos-load    \
+	illumina-dump   \
+	illumina-load   \
+	kar             \
+	kdbmeta         \
+	kget            \
+	latf-load       \
+	prefetch        \
+	rcexplain       \
+	remote-fuser    \
+	sam-dump        \
+	sff-dump        \
+	sff-load        \
+	srapath         \
+	sra-pileup      \
+	sra-sort        \
+	sra-stat        \
+	srf-load        \
+	test-sra        \
+	vdb-config      \
+	vdb-copy        \
+	vdb-decrypt     \
+	vdb-dump        \
+	vdb-encrypt     \
+	vdb-lock        \
+	vdb-passwd      \
+	vdb-unlock      \
+	vdb-validate    \
+	sra-toolkit     \
+

build/Makefile.vers

@@ -22,5 +22,5 @@
 #
 # ===========================================================================
 
-# NCBI-VDB and library version
+# SRA-TOOLS and library version
 VERSION = 2.9.1