Commit 6881a000 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 2.6.2

parent 82d7c331
......@@ -26,5 +26,59 @@
The NCBI SRA Software Development Kit
Contact: sra-tools@ncbi.nlm.nih.gov
Release documentation is now being delivered at
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
NCBI External Developer Release: SRA Toolkit 2.6.2
April 20, 2016
align-cache: a tool producing vdbcache that reduces effects of random access and improves speed.
bam-load: Fixed bug in validation code for unsorted bam files
bam-load: If two (or more) local reference names refer to the same global reference,
bam-load will record the first one used and report the change.
bam-load: Secondary alignment will be used for spot assembly if the loader is explicitly told to use them
bam-load: The code that had invalid item in index problem was removed in the process of addressing a performance issue.
bam-load: change reporting of fatal warnings into fatal errors
bam-load: changed from an error to a warning if using secondary alignments to create spots
bam-load: low-match secondary alignments are now discarded; low-match primary alignments are logged,
and if too many, it will abort the load.
bam-load: records the contents of the BX tag
bam-load: rules for spot assembly were reverted to assembling spots only on primary alignments
blast, build: Improved blast tools: all required libraries are linked statically.
build: Allow to build sra-tools on systems without static c++ library
check-corrupt, vdb-validate: Added a new set of checks that can be triggered by using one of two "--sdc:" cmd options
copycat: now runs on Centos 7; no longer uses system-installed magic file
dbgap-mount: Added support for standard options "-L" and "-o", which allow users
to determine the logging level and log output file
dbgap-mount: New optional parameter was introduced '-u' which allows user
to unmount FUSE/DOKAN volume. Implemented on linux and windows
fastq-load: The (old) fastq-loader will properly report multiple reads on the 454 platform (and still fail).
kar: added '--md5' option to create md5sum compatible auxiliary file
kdb: Fixed VTableDropColumn, so that it can drop static columns
kfs, kns, ngs, sra-tools: Fixed thread safety issues for both cache and http files
kget: kget has a new option --full to match wget in speed. added examples.sh
kproc: Fixed KQueue to wake waiters when sealed, fixed KSemaphore to wake waiters when canceled
latf-load: now allows undescores inside spot group names
latf-load: now loads data produced by fastq-dump
latf-load: updated to support Illumina tag line format with identifier at the front
pileup-stats: added -V (--version) option: prints out the software
pileup-stats: pileup-stats: added version support (options -V or --version)
prefetch: Added --eliminate-quals option which speeds up HTTP download by ignoring QUALITY column`s data
prefetch: Fixed failure when running prefetch.exe "-a<bin|key>" when there is a space after "-a"
prefetch: messages about maximum size of download are made more user-friendly.
prefetch: now will download even when caching is disabled
ref-variation: --input-file option allows to specify input accessions and paths in the file
ref-variation: added "count-strand" option: it controls relative orientation of 3' and 5' fragments.
ref-variation: added -c option to flush output immediately; reporting zero matches
ref-variation: added a way to specify a number of repeats of the query
ref-variation: improved threading management
ref-variation: removed irrelevant warnings reported in some cases in debug version only
sam-dump: Segfault no longer occurs when confronted with large amounts of header lines
sam-dump: added option to produce MD tags
sam-dump: filters out duplicates in the rows that it generates
sam-dump: produces BX-tags if preserved in SRA file by bam-load
sra-sort: correctly generates spot-id column even in the absence of primary alignments
sra-stat: no longer fails when CS_NATIVE column is not present.
sra-tools, vdb-config: Removed dependency of mac binaries on unnecessary libraries, e.g. libxml2.
sra-tools: https://github.com/ncbi/sra-tools/issues/27 : contains short and long examples of how to configure sra-tools build
var-expand: a tool for batch variation expansion
vdb-config: now handles standard options such as --option-file
vdb-validate: Added code to continue with the next row when column has discontiguous blobs
# NCBI External Developer Release:
## SRA Toolkit 2.6.2
**April 20, 2016**
**align-cache**: a tool producing vdbcache that reduces effects of random access and improves speed.
**bam-load**: Fixed bug in validation code for unsorted bam files
**bam-load**: If two (or more) local reference names refer to the same global reference, bam-load will record the first one used and report the change.
**bam-load**: Secondary alignment will be used for spot assembly if the loader is explicitly told to use them
**bam-load**: The code that had invalid item in index problem was removed in the process of addressing a performance issue.
**bam-load**: change reporting of fatal warnings into fatal errors
**bam-load**: changed from an error to a warning if using secondary alignments to create spots
**bam-load**: low-match secondary alignments are now discarded; low-match primary alignments are logged, and if too many, it will abort the load.
**bam-load**: records the contents of the BX tag
**bam-load**: rules for spot assembly were reverted to assembling spots only on primary alignments
**blast, build**: Improved blast tools: all required libraries are linked statically.
**build**: Allow to build sra-tools on systems without static c++ library
**check-corrupt, vdb-validate**: Added a new set of checks that can be triggered by using one of two "--sdc:" cmd options
**copycat**: now runs on Centos 7; no longer uses system-installed magic file
**dbgap-mount**: Added support for standard options "-L" and "-o", which allow users to determine the logging level and log output file
**dbgap-mount**: New optional parameter was introduced '-u' which allows user to unmount FUSE/DOKAN volume. Implemented on linux and windows
**fastq-load**: The (old) fastq-loader will properly report multiple reads on the 454 platform (and still fail).
**kar**: added '--md5' option to create md5sum compatible auxiliary file
**kdb**: Fixed VTableDropColumn, so that it can drop static columns
**kfs, kns, ngs, sra-tools**: Fixed thread safety issues for both cache and http files
**kget**: has a new option --full to match wget in speed. added examples.sh
**kproc**: Fixed KQueue to wake waiters when sealed, fixed KSemaphore to wake waiters when canceled
**latf-load**: now allows undescores inside spot group names
**latf-load**: now loads data produced by fastq-dump
**latf-load**: updated to support Illumina tag line format with identifier at the front
**pileup-stats**: added -V (--version) option: prints out the software
**pileup-stats**: pileup-stats: added version support (options -V or --version)
**prefetch**: Added --eliminate-quals option which speeds up HTTP download by ignoring QUALITY column`s data
**prefetch**: Fixed failure when running prefetch.exe "-a<bin|key>" when there is a space after "-a"
**prefetch**: messages about maximum size of download are made more user-friendly.
**prefetch**: now will download even when caching is disabled
**ref-variation**: --input-file option allows to specify input accessions and paths in the file
**ref-variation**: added "count-strand" option: it controls relative orientation of 3' and 5' fragments.
**ref-variation**: added -c option to flush output immediately; reporting zero matches
**ref-variation**: added a way to specify a number of repeats of the query
**ref-variation**: improved threading management
**ref-variation**: removed irrelevant warnings reported in some cases in debug version only
**sam-dump**: Segfault no longer occurs when confronted with large amounts of header lines
**sam-dump**: added option to produce MD tags
**sam-dump**: filters out duplicates in the rows that it generates
**sam-dump**: produces BX-tags if preserved in SRA file by bam-load
**sra-sort**: correctly generates spot-id column even in the absence of primary alignments
**sra-stat**: no longer fails when CS_NATIVE column is not present.
**sra-tools, vdb-config**: Removed dependency of mac binaries on unnecessary libraries, e.g. libxml2.
**sra-tools**: [https://github.com/ncbi/sra-tools/issues/27](https://github.com/ncbi/sra-tools/issues/27) : contains short and long examples of how to configure sra-tools build
**var-expand**: a tool for batch variation expansion
**vdb-config**: now handles standard options such as --option-file
**vdb-validate**: Added code to continue with the next row when column has discontiguous blobs
......@@ -74,7 +74,7 @@ uninstall:
#-------------------------------------------------------------------------------
# clean
#
clean: clean_test
clean: clean_deb clean_rpm clean_test
clean_test:
@ $(MAKE) -s -C test clean
......@@ -97,6 +97,40 @@ 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
#
......
......@@ -30,6 +30,8 @@ Contact: sra-tools@ncbi.nlm.nih.gov
SRA Tools web site: http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc
Download page: https://github.com/ncbi/sra-tools/wiki/Downloads
Please check the CHANGES file for change history.
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
using data in the INSDC Sequence Read Archives.
......
......@@ -2,11 +2,14 @@
### Contact:
email: sra-tools@ncbi.nlm.nih.gov
or visit the [SRA Tools web site](http://ncbi.github.io/sra-tools) - UPDATED
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.
## 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.
......
.cvsignore
RHOST* ARCH* BUILD* COMP* OUTDIR*
STATIC
ld.linux.exe_cmd.sh
LNKG.*
Makefile.config*
\ No newline at end of file
Makefile.config*
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
<ProjectConfiguration Include="Debug|Win32">
<Configuration>Debug</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|Win32">
<Configuration>Release</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
</ItemGroup>
<Import Project=".\exe-project.props" />
<ItemDefinitionGroup>
<Link>
<AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>$(VDB_TARGET)lib\zlib.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>$(VDB_TARGET)lib\kapp.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>$(VDB_TARGET)lib\libxfs.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>%ProgramFiles(x86)%\Dokan\DokanLibrary\dokan.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>Kernel32.lib;%(AdditionalDependencies)</AdditionalDependencies>
<AdditionalDependencies>Shlwapi.lib;%(AdditionalDependencies)</AdditionalDependencies>
</Link>
</ItemDefinitionGroup>
<ItemGroup>
<ClCompile Include="..\..\..\tools\dbgap-mount\dbgap-mount-tool.c" />
<ClCompile Include="..\..\..\tools\dbgap-mount\win\wrap.c" />
</ItemGroup>
<PropertyGroup Label="Globals">
<ProjectGuid>{8DA91267-49B1-4696-AF9D-2A98B697167E}</ProjectGuid>
</PropertyGroup>
</Project>
......@@ -24,6 +24,7 @@
<ItemDefinitionGroup>
<Link>
<AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
<EntryPointSymbol>wmainCRTStartupNoPathConversion</EntryPointSymbol>
</Link>
</ItemDefinitionGroup>
......
......@@ -22,7 +22,8 @@
<Import Project=".\test-project.props" />
<Target Name="AfterBuild" Condition="'$(Autorun)'=='true'">
<Exec Command="$(VDB_TARGET)\bin\align-info -h" WorkingDirectory="$(ProjectDir)"/>
<Exec Command="dir . $(VDB_TARGET)\bin\align-info.exe"/>
<Exec Command="$(VDB_TARGET)\bin\align-info.exe -h" WorkingDirectory="$(ProjectDir)"/>
</Target>
</Project>
\ No newline at end of file
</Project>
......@@ -37,7 +37,8 @@
</ItemGroup>
<Target Name="AfterBuild" Condition="'$(Autorun)'=='true'">
<Exec Command="$(OutDir)vdb-config$(TargetExt) --root -s vdb/schema/paths=&quot;../../../../ncbi-vdb/interfaces&quot;"/>
<Exec Command="$(OutDir)$(TargetName)$(TargetExt)" WorkingDirectory="$(ProjectDir)"/>
</Target>
</Project>
\ No newline at end of file
</Project>
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
<PropertyGroup Label="Configuration">
<PlatformToolset>v100</PlatformToolset>
</PropertyGroup>
<PropertyGroup Label="Globals">
<Platform Condition="'$(Platform)' == ''">x64</Platform>
<Configuration Condition="'$(Configuration)' == ''">Release</Configuration>
<NGS_ROOT Condition="'$(NGS_ROOT)' == ''">$(ProjectDir)..\..\..\..\ngs\ngs-sdk\</NGS_ROOT>
<NGS_OUTDIR Condition="'$(NGS_OUTDIR)' == ''">$(NGS_ROOT)..\..\OUTDIR\</NGS_OUTDIR>
<NGS_TARGET Condition="'$(NGS_TARGET)' == ''">$(NGS_OUTDIR)win\cl\$(Platform)\$(Configuration)\</NGS_TARGET>
<NGS_TARGET Condition="'$(NGS_TARGET)' == ''">$(NGS_OUTDIR)win\$(PlatformToolset)\$(Platform)\$(Configuration)\</NGS_TARGET>
<VDB_OUTDIR Condition="'$(VDB_OUTDIR)' == ''">$(NGS_OUTDIR)</VDB_OUTDIR>
<VDB_ROOT Condition="'$(VDB_ROOT)' == ''">$(ProjectDir)..\..\..\..\ncbi-vdb\</VDB_ROOT>
<VDB_TARGET Condition="'$(VDB_TARGET)' == ''">$(VDB_OUTDIR)win\cl\$(Platform)\$(Configuration)\</VDB_TARGET>
<VDB_TARGET Condition="'$(VDB_TARGET)' == ''">$(VDB_OUTDIR)win\$(PlatformToolset)\$(Platform)\$(Configuration)\</VDB_TARGET>
</PropertyGroup>
......
......@@ -39,6 +39,8 @@
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump-redir.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump-str.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump-tools.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump-interact.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump-repo.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb-dump.c" />
<ClCompile Include="..\..\..\tools\vdb-dump\vdb_info.c" />
</ItemGroup>
......
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#VERBOSE=-v
# determine shell environment ($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
TOOLS_TO_INSTALL += remote-fuser
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): $(DST)/etc/ncbi/default.kfg $(DST)/etc/ncbi/schema.kfg \
$(DST)/etc/ncbi/vdb-copy.kfg $(DST)/usr/bin $(DST)/DEBIAN/control
ifeq (mac,$(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/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
......@@ -79,11 +79,11 @@ ifeq (dbg, $(BUILD))
PED = -std=gnu99 -pedantic # -fdiagnostics-show-option
else
OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1
ifeq (x86_64, $(ARCH))
OPT += -Wall
endif
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))
......
......@@ -33,46 +33,10 @@ include $(TOP)/build/Makefile.$(OS)
#-------------------------------------------------------------------------------
# install
#
TOOLS_TO_INSTALL = \
abi-dump \
abi-load \
align-info \
bam-load \
cache-mgr \
cg-load \
fastq-dump \
fastq-load \
helicos-load \
illumina-dump \
illumina-load \
kar \
kdbmeta \
latf-load \
prefetch \
rcexplain \
sam-dump \
sff-dump \
sff-load \
sra-pileup \
sra-sort \
sra-stat \
srapath \
srf-load \
test-sra \
vdb-config \
vdb-copy \
vdb-decrypt \
vdb-dump \
vdb-encrypt \
vdb-lock \
vdb-passwd \
vdb-unlock \
vdb-validate \
#
# remote-fuser \
# blastn_vdb \
# tblastn_vdb \
# $TOOLS_TO_INSTALL
include $(TOP)/build/Makefile.tools
#fake root for debugging
#uncomment this line and change the test for root ( see under install: ) to succeed:
......@@ -85,6 +49,8 @@ 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"
$(TOOLS_TO_INSTALL):
@ printf "Installing $@..."
......@@ -102,9 +68,9 @@ endif
install: installexes
ifeq (true, $(LINUX_ROOT))
@ # install configuration file(s)
@ echo "Installing configuration files to $(ROOT)/etc/ncbi/"
@ echo "Installing configuration files to $(ROOT)/etc/ncbi/..."
@ mkdir -p $(ROOT)/etc/ncbi/
@ cp $(TOP)/tools/vdb-copy/vdb-copy.kfg $(ROOT)/etc/ncbi/
@ cp $(TOP)/tools/vdb-copy/vdb-copy.kfg $(ROOT)/etc/ncbi/ && echo "done"
@ #
@ echo "Updating $(PROFILE_FILE).[c]sh"
@ printf \
......@@ -130,7 +96,7 @@ endif
# uninstall
#
TO_UNINSTALL = $(addsuffix *,$(addprefix $(INST_BINDIR)/,$(TOOLS_TO_INSTALL)))
TO_UNINSTALL = $(addsuffix *,$(addprefix $(INST_BINDIR)/,$(TOOLS_TO_INSTALL) magic))
TO_UNINSTALL_AS_ROOT = $(ROOT)/etc/ncbi/vdb-copy.kfg $(PROFILE_FILE).sh $(PROFILE_FILE).csh
uninstall:
......
......@@ -72,3 +72,16 @@ COMPILERS = GCC # ICC
# copy without following symlinks
COPY = cp -P
# valgrind
VALGRIND = export NCBI_VALGRIND=ncbi; valgrind --error-exitcode=1 --suppressions=$(TOP)/build/valgrind.suppress --show-reachable=no
VALGRIND_TARGETS = $(addprefix vg-,$(TEST_TOOLS))
valgrind: $(VALGRIND_TARGETS)
vg-test-%: test-%
$(VALGRIND) $(TEST_BINDIR)/$^
vg-wb-test-%: wb-test-%
$(VALGRIND) $(TEST_BINDIR)/$^
# ===========================================================================
#
# 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
TOOLS_TO_INSTALL += remote-fuser
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: