Commit 62d125bb75d5dacf9256ff34b2d3a3deb65d5757 - ngs-sdk

+15

-0

CHANGES less more

25	25	The NCBI NGS Software Development Kit
26	26	Contact: sra-tools@ncbi.nlm.nih.gov
27	27
	28	NCBI External Developer Release: NGS SDK 1.2.5
	29	July 11, 2016
	30
	31	blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
	32	htsjdk: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK
	33	kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME
	34	ngs, search, sra-search: sra-search was modified to support multiple threads.
	35	ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored
	36	ngs-engine: Added support for blob-by-blob access to SEQUENCE table
	37	ngs-engine: removed a potential memory leak in NGS_CursorMake()
	38	ngs: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs
	39	ngs: now supports parallel compilation with "make -j N"
	40	vfs: environment variable VDB_PWFILE is no longer used
	41
	42
28	43	NCBI External Developer Release: NGS SDK 1.2.4
29	44	May 25, 2016
30	45

+26

-11

CHANGES.md less more

0	0	# NCBI External Developer Release:
	1
	2	## NGS SDK 1.2.5
	3	July 12, 2016
	4
	5	blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
	6	htsjdk: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK
	7	kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME
	8	ngs, search, sra-search: sra-search was modified to support multiple threads.
	9	ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored
	10	ngs-engine: Added support for blob-by-blob access to SEQUENCE table
	11	ngs-engine: removed a potential memory leak in NGS_CursorMake()
	12	ngs: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs
	13	ngs: now supports parallel compilation with "make -j N"
	14	vfs: environment variable VDB_PWFILE is no longer used
	15
1	16
2	17	## NGS SDK 1.2.4
3	18	May 25, 2016
4	19
5		build: MSVS 2013 toolset (12.0) is now supported across all repositories
6		doc, ngs: updated javadoc to include throws and other missing tags
7		examples, ngs: added DumpReferenceFASTA.py example
8		htsjdk: added code to HTS-JDK to avoid involving NGS unless we are sure that it is being requested
9		ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments
10		ngs, test: ngs-python: fixed bug in String processing for Python 3.*
11		ngs-engine: ncbi-ngs engine was updated: fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
12		ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries
13		ngs: Python code will check for the latest version of the libraries and update if newer ones are available
14		ngs: check for the latest version of the libraries and update if newer ones are available
15		ngs: simplified ngs-python bindings
	20	build: MSVS 2013 toolset (12.0) is now supported across all repositories
	21	doc, ngs: updated javadoc to include throws and other missing tags
	22	examples, ngs: added DumpReferenceFASTA.py example
	23	htsjdk: added code to HTS-JDK to avoid involving NGS unless we are sure that it is being requested
	24	ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments
	25	ngs, test, ngs-python: fixed bug in String processing for Python 3.x
	26	ngs-engine: ncbi-ngs engine was updated - fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
	27	ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries
	28	ngs: Python code will check for the latest version of the libraries and update if newer ones are available
	29	ngs: check for the latest version of the libraries and update if newer ones are available
	30	ngs: simplified ngs-python bindings

+1

-0

ngs-bam/.gitignore less more

	0	/ld.linux.exe_cmd.sh
0	1	/Makefile.config*
1	2	/reconfigure

+1

-1

ngs-bam/Makefile less more

39	39
40	40	install: Makefile.config
41	41	@ $(MAKE) -f Makefile.libs
42		@ perl $(TOP)/setup/install
	42	@ $(MAKE) -s --no-print-directory -f Makefile.install install
43	43
44	44	.PHONY: std clean install

+121

-0

ngs-bam/Makefile.install less more

	0	# ===========================================================================
	1	#
	2	# PUBLIC DOMAIN NOTICE
	3	# National Center for Biotechnology Information
	4	#
	5	# This software/database is a "United States Government Work" under the
	6	# terms of the United States Copyright Act. It was written as part of
	7	# the author's official duties as a United States Government employee and
	8	# thus cannot be copyrighted. This software/database is freely available
	9	# to the public for use. The National Library of Medicine and the U.S.
	10	# Government have not placed any restriction on its use or reproduction.
	11	#
	12	# Although all reasonable efforts have been taken to ensure the accuracy
	13	# and reliability of the software and data, the NLM and the U.S.
	14	# Government do not and cannot warrant the performance or results that
	15	# may be obtained by using this software or data. The NLM and the U.S.
	16	# Government disclaim all warranties, express or implied, including
	17	# warranties of performance, merchantability or fitness for any particular
	18	# purpose.
	19	#
	20	# Please cite the author in any work or product based on this material.
	21	#
	22	# ===========================================================================
	23
	24	default: install
	25
	26	TOP ?= $(CURDIR)
	27	MODPATH =
	28
	29	include $(TOP)/Makefile.config
	30
	31	#-------------------------------------------------------------------------------
	32	# install
	33	#
	34	LIBRARIES_TO_INSTALL = \
	35	ngs-bam.$(VERSION_SHLX) \
	36	ngs-bam-c++.$(VERSION_LIBX) \
	37
	38	LIB_TARGET = $(INST_LIBDIR)$(BITS)
	39
	40	LIBRARIES_WITH_PREFIX = \
	41	$(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL))
	42
	43	copylibs: $(LIB_TARGET)
	44	@ echo "Installing libraries to $(LIB_TARGET)"
	45	@ $(MAKE) -f Makefile.install $(LIBRARIES_WITH_PREFIX)
	46
	47	copyincludes:
	48	@ echo "Installing includes to $(INST_INCDIR)"
	49	@ mkdir -p $(INST_INCDIR)/
	50	@ cp -r $(TOP)/ngs-bam $(INST_INCDIR)/
	51
	52	copyexamples:
	53	ifneq ($(INST_SHAREDIR),)
	54	@ echo "Installing examples to $(INST_SHAREDIR)"
	55	@ mkdir -p $(INST_SHAREDIR)/examples
	56	@ $(MAKE) -C $(TOP)/examples install INST_TARGET=$(INST_SHAREDIR)/examples
	57	endif
	58
	59	#fake root for debugging
	60	#uncomment this line and change the test for root ( see under install: ) to succeed:
	61	#ROOT = ~/root
	62
	63	INCLUDE_SYMLINK = $(ROOT)/usr/include/ngs-bam
	64	PROFILE_FILE = $(ROOT)/etc/profile.d/ngs-bam
	65
	66	ifeq (linux, $(OS))
	67	ifeq (0, $(shell id -u))
	68	LINUX_ROOT = true
	69	endif
	70	endif
	71
	72	install: copylibs copyincludes copyexamples
	73	ifeq (true, $(LINUX_ROOT))
	74	@ # install symlink to includes
	75	@ echo "Updating $(INCLUDE_SYMLINK)"
	76	@ rm -f $(INCLUDE_SYMLINK)
	77	@ ln -s $(INST_INCDIR)/ngs-bam $(INCLUDE_SYMLINK)
	78	@ #
	79	@ echo "Updating $(PROFILE_FILE).[c]sh"
	80	@ printf \
	81	"#version $(VERSION)\n"\
	82	"if ! echo \$$LD_LIBRARY_PATH \| /bin/grep -q $(LIB_TARGET)\n"\
	83	"then export LD_LIBRARY_PATH=$(LIB_TARGET):\$$LD_LIBRARY_PATH\n"\
	84	"fi\n"\
	85	"export NGS_LIBDIR=$(LIB_TARGET)\n" \
	86	>$(PROFILE_FILE).sh && chmod 644 $(PROFILE_FILE).sh \|\| true;
	87	@ printf \
	88	"#version $(VERSION)\n"\
	89	"echo \$$LD_LIBRARY_PATH \| /bin/grep -q $(LIB_TARGET)\n"\
	90	"if ( \$$status ) setenv LD_LIBRARY_PATH $(LIB_TARGET):\$$LD_LIBRARY_PATH\n"\
	91	"setenv NGS_LIBDIR $(LIB_TARGET)\n" \
	92	>$(PROFILE_FILE).csh && chmod 644 $(PROFILE_FILE).csh \|\| true;
	93	@ #TODO: check version of the files above
	94	@ #
	95	@ echo "Use \$$NGS_LIBDIR in your link commands, e.g.:"
	96	@ echo " ld -L\$$NGS_LIBDIR -lngs-bam ..."
	97	else
	98	@ #
	99	@ echo "Please add $(LIB_TARGET) to your LD_LIBRARY_PATH, e.g.:"
	100	@ echo " export LD_LIBRARY_PATH=$(LIB_TARGET):\$$LD_LIBRARY_PATH"
	101	@ #
	102	@ echo "Use $(LIB_TARGET) in your link commands, e.g.:"
	103	@ echo " export NGS_LIBDIR=$(LIB_TARGET)"
	104	@ echo " ld -L\$$NGS_LIBDIR -lngs-bam ..."
	105	endif
	106
	107	TO_UNINSTALL = $(LIB_TARGET)/libngs-bam* $(INST_INCDIR)/ngs-bam $(INST_SHAREDIR)/examples
	108	TO_UNINSTALL_AS_ROOT = $(INST_INCDIR)/ngs-bam $(INCLUDE_SYMLINK) $(PROFILE_FILE).*
	109
	110	uninstall:
	111	@ echo "Uninstalling $(TO_UNINSTALL) ..."
	112	@ rm -rf $(TO_UNINSTALL)
	113	ifeq (true, $(LINUX_ROOT))
	114	@ echo "Uninstalling $(TO_UNINSTALL_AS_ROOT) ..."
	115	@ rm -rf $(TO_UNINSTALL_AS_ROOT)
	116	endif
	117	@ echo "done."
	118
	119	.PHONY: install copylibs copyincludes copyexamples uninstall
	120

+26

-0

ngs-bam/Makefile.vers less more

	0	# ===========================================================================
	1	#
	2	# PUBLIC DOMAIN NOTICE
	3	# National Center for Biotechnology Information
	4	#
	5	# This software/database is a "United States Government Work" under the
	6	# terms of the United States Copyright Act. It was written as part of
	7	# the author's official duties as a United States Government employee and
	8	# thus cannot be copyrighted. This software/database is freely available
	9	# to the public for use. The National Library of Medicine and the U.S.
	10	# Government have not placed any restriction on its use or reproduction.
	11	#
	12	# Although all reasonable efforts have been taken to ensure the accuracy
	13	# and reliability of the software and data, the NLM and the U.S.
	14	# Government do not and cannot warrant the performance or results that
	15	# may be obtained by using this software or data. The NLM and the U.S.
	16	# Government disclaim all warranties, express or implied, including
	17	# warranties of performance, merchantability or fitness for any particular
	18	# purpose.
	19	#
	20	# Please cite the author in any work or product based on this material.
	21	#
	22	# ===========================================================================
	23
	24	# NGS-BAM and library version
	25	VERSION = 1.2.5

+124

-82

ngs-bam/setup/konfigure.perl less more

202	202	exit 1;
203	203	}
204	204
	205	my $OS_DISTRIBUTOR = '';
	206	if ($OS eq 'linux') {
	207	print "checking OS distributor... " unless ($AUTORUN);
	208	$OS_DISTRIBUTOR = `lsb_release -si 2> /dev/null`;
	209	chomp $OS_DISTRIBUTOR;
	210	println $OS_DISTRIBUTOR unless ($AUTORUN);
	211	}
	212
205	213	print "checking machine architecture... " unless ($AUTORUN);
206	214	println $MARCH unless ($AUTORUN);
207	215	unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /i?86/i) {

282	290
283	291	my $TOOLS = "";
284	292	$TOOLS = "jdk" if ($PKG{LNG} eq 'JAVA');
285
286		print "checking $PACKAGE_NAME version... " unless ($AUTORUN);
287		my $FULL_VERSION = VERSION();
288		println $FULL_VERSION unless ($AUTORUN);
289	293
290	294	# determine architecture
291	295

423	427	$NO_ARRAY_BOUNDS_WARNING = '-Wno-array-bounds';
424	428	}
425	429
	430	my $STATIC_LIBSTDCPP = '';
	431	if ($TOOLS =~ /gcc$/) {
	432	$STATIC_LIBSTDCPP = check_static_libstdcpp();
	433	}
	434
426	435	my @dependencies;
427	436
428	437	my %DEPEND_OPTIONS;

463	472	$href->{locbldpath} = expand($href->{locbldpath}) if ($href->{locbldpath});
464	473
465	474	# found directories
466		my ($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar);
	475	my
	476	($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar, $found_src);
467	477
468	478	my %a = %$href;
469	479	next if ($a{option} && $DEPEND_OPTIONS{$a{option}});

476	486	my $need_itf = ! ($a{type} =~ /D/ \|\| $a{type} =~ /E/ \|\| $a{type} =~ /J/);
477	487	my $need_jar = $a{type} =~ /J/;
478	488
479		my ($bin, $inc, $lib, $ilib)
480		= ($a{bin}, $a{include}, $a{lib}); # file names to check
	489	my ($bin, $inc, $lib, $ilib, $src)
	490	= ($a{bin}, $a{include}, $a{lib}, undef, $a{src}); # file names to check
481	491	$lib = '' unless ($lib);
482	492	$lib = expand($lib);
483	493

519	529	undef $il;
520	530	++$has_option{sources};
521	531	}
522		my ($fi, $fl, $fil) = find_in_dir($try, $i, $l, $il);
	532	my ($fi, $fl, $fil)
	533	= find_in_dir($try, $i, $l, $il, undef, undef, $src);
523	534	if ($fi \|\| $fl \|\| $fil) {
524	535	$found_itf = $fi if (! $found_itf && $fi);
525	536	$found_lib = $fl if (! $found_lib && $fl);

540	551	}
541	552	if (! $found_itf && ! $has_option{sources} && $a{srcpath}) {
542	553	my $try = $a{srcpath};
543		($found_itf) = find_in_dir($try, $inc);
	554	($found_itf, undef, undef, $found_src)
	555	= find_in_dir($try, $inc, undef, undef, undef, undef, $src);
544	556	}
545	557	if (! $has_option{prefix}) {
546	558	my $try = $a{pkgpath};

667	679	push(@dependencies, "$a{aname}_INCDIR = $found_itf");
668	680	println "includes: $found_itf";
669	681	}
	682	if ($found_src) {
	683	$found_src = abs_path($found_src);
	684	push(@dependencies, "$a{aname}_SRCDIR = $found_src");
	685	println "sources: $found_src";
	686	}
670	687	if ($found_lib) {
671	688	$found_lib = abs_path($found_lib);
672	689	if ($a{aname} eq 'NGS' \|\| $a{aname} eq 'VDB') {

698	715	}
699	716	}
700	717
701		my ($E_BINDIR, $E_LIBDIR, $VERSION, $MAJVERS, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
702		$E_VERSION_EXEX, $E_MAJVERS_EXEX)
	718	my ($E_BINDIR, $E_LIBDIR, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
	719	$E_VERSION_EXEX, $E_MAJVERS_EXEX)
703	720	= ('' , '');
704	721
705	722	println unless ($AUTORUN);

710	727	println "configure: creating '$COMP' ($TOOLS)" unless ($AUTORUN);
711	728	open F, ">$COMP" or die "cannot open $COMP to write";
712	729	print F "$TOOLS\n";
	730	close F;
	731	}
	732
	733	if ($TOOLS =~ /gcc$/) {
	734	my $EXECMDF = File::Spec->catdir(CONFIG_OUT(), 'ld.linux.exe_cmd.sh');
	735	println "configure: creating '$EXECMDF'" unless ($AUTORUN);
	736	open F, ">$EXECMDF" or die "cannot open $EXECMDF to write";
	737	print F "EXE_CMD=\"\$LD $STATIC_LIBSTDCPP -static-libgcc\"\n";
713	738	close F;
714	739	}
715	740

772	797	# target OS
773	798	OS = $OS
774	799	OSINC = $OSINC
	800	OS_DISTRIBUTOR = $OS_DISTRIBUTOR
775	801
776	802	# prefix string for system libraries
777	803	LPFX = $LPFX

865	891	L($F, "NO_ARRAY_BOUNDS_WARNING = $NO_ARRAY_BOUNDS_WARNING");
866	892	L($F);
867	893
868		# version information
869
870		my $MAJMIN;
871
872		if ($FULL_VERSION =~ /(\d+)\.(\d+)\.(\d+)-?\w\d/) {
873		$VERSION = "$1.$2.$3";
874		$MAJMIN = "$1.$2";
875		$MAJVERS = $1;
876		} else {
877		die $VERSION;
878		}
879
880	894	print $F <<EndText;
881		# $PACKAGE_NAME and library version
882		VERSION = $VERSION
883		MAJMIN = $MAJMIN
884		MAJVERS = $MAJVERS
	895	# \$(VERSION) is defined in a separate file which is updated every release
	896	include \$(TOP)/Makefile.vers
	897
	898	empty :=
	899	space := \$(empty) \$(empty)
	900	MAJMIN = \$(subst \$(space),.,\$(wordlist 1,2,\$(subst .,\$(space),\$(VERSION))))
	901	MAJVERS = \$(firstword \$(subst .,\$(space),\$(VERSION)))
885	902
886	903	# output path
887	904	BUILD_PREFIX = $BUILD_PREFIX

971	988	L($F, 'include $(wildcard $(CLSDIR)/*.d)');
972	989	}
973	990	L($F, $_) foreach (@dependencies);
	991	L($F);
	992
	993	# pass HAVE_XML2 to build scripts
	994	L($F, 'ifeq (,$(HAVE_XML2))');
	995	L($F, ' HAVE_XML2=0');
	996	L($F, 'endif');
	997	L($F, 'CONFIGURE_FOUND_XML2=$(HAVE_XML2)');
	998	L($F, 'export CONFIGURE_FOUND_XML2');
974	999	L($F);
975	1000
976	1001	if ($OS eq 'linux' \|\| $OS eq 'mac') {

1038	1063	T($F, ' fi');
1039	1064	}
1040	1065	close $F;
1041
1042		# create Makefile.config.install
1043		println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
1044		open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
1045
1046		$OPT{'javadir' } = '' unless ($OPT{'javadir' });
1047		$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
1048
1049		print $F "sub CONFIGURE {\n";
1050		print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
1051		print $F " \$_{VERSION } = '$VERSION';\n";
1052		print $F " \$_{LNG } = '$PKG{LNG}';\n";
1053		print $F " \$_{OS } = '$OS';\n";
1054		print $F " \$_{BITS } = $BITS;\n";
1055		print $F " \$_{MAJVERS } = $MAJVERS;\n";
1056		print $F " \$_{LPFX } = '$LPFX';\n";
1057		print $F " \$_{LIBX } = '$LIBX';\n";
1058		print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
1059		print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
1060		print $F " \$_{SHLX } = '$SHLX';\n";
1061		print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
1062		print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
1063		print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
1064		print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
1065		print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
1066		if ($PKG{LNG} ne 'PYTHON') {
1067		print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
1068		print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
1069		} elsif ($OPT{PYTHON_LIB_PATH}) {
1070		print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
1071		}
1072		print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
1073		print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
1074		print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
1075		print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
1076		print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
1077		print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
1078		print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
1079		print $F "\n";
1080		print $F " \@_\n";
1081		print $F "}\n";
1082		print $F "\n";
1083		print $F "1\n";
1084
1085		close $F;
	1066
	1067	# creation of Makefile.config.install is disabled, since nobody uses it now
	1068	# and I need to remove versions from prl scripts
	1069	if (0) {
	1070	# create Makefile.config.install
	1071	println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
	1072	open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
	1073
	1074	$OPT{'javadir' } = '' unless ($OPT{'javadir' });
	1075	$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
	1076
	1077	print $F "sub CONFIGURE {\n";
	1078	print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
	1079	print $F " \$_{VERSION } = '\$VERSION';\n";
	1080	print $F " \$_{LNG } = '$PKG{LNG}';\n";
	1081	print $F " \$_{OS } = '$OS';\n";
	1082	print $F " \$_{BITS } = $BITS;\n";
	1083	print $F " \$_{MAJVERS } = \$MAJVERS;\n";
	1084	print $F " \$_{LPFX } = '$LPFX';\n";
	1085	print $F " \$_{LIBX } = '$LIBX';\n";
	1086	print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
	1087	print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
	1088	print $F " \$_{SHLX } = '$SHLX';\n";
	1089	print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
	1090	print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
	1091	print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
	1092	print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
	1093	print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
	1094	if ($PKG{LNG} ne 'PYTHON') {
	1095	print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
	1096	print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
	1097	} elsif ($OPT{PYTHON_LIB_PATH}) {
	1098	print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
	1099	}
	1100	print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
	1101	print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
	1102	print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
	1103	print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
	1104	print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
	1105	print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
	1106	print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
	1107	print $F "\n";
	1108	print $F " \@_\n";
	1109	print $F "}\n";
	1110	print $F "\n";
	1111	print $F "1\n";
	1112
	1113	close $F;
	1114	}
1086	1115	}
1087	1116
1088	1117	if (! $OPT{'status'} ) {

1253	1282	}
1254	1283
1255	1284	sub find_in_dir {
1256		my ($dir, $include, $lib, $ilib, $jar, $bin) = @_;
	1285	my ($dir, $include, $lib, $ilib, $jar, $bin, $src) = @_;
1257	1286	unless (-d $dir) {
1258		# println "no" unless ($AUTORUN);
1259	1287	println "\t\tnot found $dir" if ($OPT{'debug'});
1260	1288	return;
1261	1289	}
1262		# print "\t$dir... " unless ($AUTORUN);
1263		# print "[found] " if ($OPT{'debug'});
1264		my ($found_inc, $found_lib, $found_ilib);
	1290	my ($found_inc, $found_lib, $found_ilib, $found_src);
1265	1291	if ($include) {
1266	1292	print "\tincludes... " unless ($AUTORUN);
1267	1293	if (-e "$dir/$include") {

1279	1305	}
1280	1306	}
1281	1307	if ($lib \|\| $ilib) {
1282		# print "\n\t" if ($nl && !$AUTORUN);
1283	1308	print "\tlibraries... " unless ($AUTORUN);
1284	1309	if ($lib) {
1285	1310	my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);

1371	1396	$found_lib = $try;
1372	1397	}
1373	1398	}
1374		return ($found_inc, $found_lib, $found_ilib);
	1399	if ($src) {
	1400	print "\tsrc... " unless ($AUTORUN);
	1401	my $try = "$dir/$src";
	1402	if (-e "$try") {
	1403	println $dir unless ($AUTORUN);
	1404	$found_src = $dir;
	1405	}
	1406	}
	1407	return ($found_inc, $found_lib, $found_ilib, $found_src);
1375	1408	}
1376	1409
1377	1410	sub reverse_build {

1409	1442	check_compiler('O', '-Wno-array-bounds');
1410	1443	}
1411	1444
	1445	sub check_static_libstdcpp {
	1446	my $option = '-static-libstdc++';
	1447	my $save = $TOOLS;
	1448	$TOOLS = $CPP;
	1449	$_ = check_compiler('O', $option);
	1450	$TOOLS = $save;
	1451	$_ ? $option : ''
	1452	}
	1453
1412	1454	sub find_lib {
1413	1455	check_compiler('L', @_);
1414	1456	}

1420	1462	if ($t eq 'L') {
1421	1463	print "checking for $n library... ";
1422	1464	} elsif ($t eq 'O') {
1423		if ($tool && $tool =~ /gcc$/) {
	1465	if ($tool && ($tool =~ /gcc$/ \|\| $tool =~ /g\+\+$/)) {
1424	1466	print "checking whether $tool accepts $n... ";
1425	1467	} else {
1426	1468	return;

1451	1493	$library = '-lmagic';
1452	1494	$log = '#include <magic.h> \n int main() { magic_open (0); }\n'
1453	1495	} elsif ($n eq 'xml2') {
1454		$library = '-lxml2';
	1496	$library = '-lxml2';
	1497	$library .= ' -liconv' if ($OS eq 'mac');
1455	1498	$log = '#include <libxml/xmlreader.h>\n' .
1456	1499	'int main() { xmlInitParser ( ); }\n'
1457	1500	} else {

1503	1546	die "No PACKAGE_NAME" unless PACKAGE_NAME();
1504	1547	die "No PACKAGE_NAMW" unless PACKAGE_NAMW();
1505	1548	die "No PACKAGE_TYPE" unless PACKAGE_TYPE();
1506		die "No VERSION" unless VERSION();
1507	1549
1508	1550	my %PKG = PKG();
1509	1551

+0

-1

ngs-bam/setup/package.prl less more

0	0	################################################################################
1	1	sub PACKAGE { 'ngs-bam' }
2		sub VERSION { '1.2.4' }
3	2	sub PACKAGE_TYPE { 'L' }
4	3	sub PACKAGE_NAME { 'NGS-BAM' }
5	4	sub PACKAGE_NAMW { 'NGS_BAM' }

+26

-0

ngs-java/Makefile.vers less more

	0	# ===========================================================================
	1	#
	2	# PUBLIC DOMAIN NOTICE
	3	# National Center for Biotechnology Information
	4	#
	5	# This software/database is a "United States Government Work" under the
	6	# terms of the United States Copyright Act. It was written as part of
	7	# the author's official duties as a United States Government employee and
	8	# thus cannot be copyrighted. This software/database is freely available
	9	# to the public for use. The National Library of Medicine and the U.S.
	10	# Government have not placed any restriction on its use or reproduction.
	11	#
	12	# Although all reasonable efforts have been taken to ensure the accuracy
	13	# and reliability of the software and data, the NLM and the U.S.
	14	# Government do not and cannot warrant the performance or results that
	15	# may be obtained by using this software or data. The NLM and the U.S.
	16	# Government disclaim all warranties, express or implied, including
	17	# warranties of performance, merchantability or fitness for any particular
	18	# purpose.
	19	#
	20	# Please cite the author in any work or product based on this material.
	21	#
	22	# ===========================================================================
	23
	24	# NGS-JAVA and library version
	25	VERSION = 1.2.5

+2

-2

ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java less more

28	28	class LibDependencies {
29	29	final static String NGS_SDK = "ngs-sdk";
30	30	final static String NCBI_VDB = "ncbi-vdb";
31		final static String NGS_SDK_VERSION = "1.2.4";
32		final static String NCBI_VDB_VERSION = "2.6.2";
	31	final static String NGS_SDK_VERSION = "1.2.5";
	32	final static String NCBI_VDB_VERSION = "2.7.0";
33	33	}

+123

-81

ngs-java/setup/konfigure.perl less more

202	202	exit 1;
203	203	}
204	204
	205	my $OS_DISTRIBUTOR = '';
	206	if ($OS eq 'linux') {
	207	print "checking OS distributor... " unless ($AUTORUN);
	208	$OS_DISTRIBUTOR = `lsb_release -si 2> /dev/null`;
	209	chomp $OS_DISTRIBUTOR;
	210	println $OS_DISTRIBUTOR unless ($AUTORUN);
	211	}
	212
205	213	print "checking machine architecture... " unless ($AUTORUN);
206	214	println $MARCH unless ($AUTORUN);
207	215	unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /i?86/i) {

282	290
283	291	my $TOOLS = "";
284	292	$TOOLS = "jdk" if ($PKG{LNG} eq 'JAVA');
285
286		print "checking $PACKAGE_NAME version... " unless ($AUTORUN);
287		my $FULL_VERSION = VERSION();
288		println $FULL_VERSION unless ($AUTORUN);
289	293
290	294	# determine architecture
291	295

423	427	$NO_ARRAY_BOUNDS_WARNING = '-Wno-array-bounds';
424	428	}
425	429
	430	my $STATIC_LIBSTDCPP = '';
	431	if ($TOOLS =~ /gcc$/) {
	432	$STATIC_LIBSTDCPP = check_static_libstdcpp();
	433	}
	434
426	435	my @dependencies;
427	436
428	437	my %DEPEND_OPTIONS;

463	472	$href->{locbldpath} = expand($href->{locbldpath}) if ($href->{locbldpath});
464	473
465	474	# found directories
466		my ($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar);
	475	my
	476	($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar, $found_src);
467	477
468	478	my %a = %$href;
469	479	next if ($a{option} && $DEPEND_OPTIONS{$a{option}});

476	486	my $need_itf = ! ($a{type} =~ /D/ \|\| $a{type} =~ /E/ \|\| $a{type} =~ /J/);
477	487	my $need_jar = $a{type} =~ /J/;
478	488
479		my ($bin, $inc, $lib, $ilib)
480		= ($a{bin}, $a{include}, $a{lib}); # file names to check
	489	my ($bin, $inc, $lib, $ilib, $src)
	490	= ($a{bin}, $a{include}, $a{lib}, undef, $a{src}); # file names to check
481	491	$lib = '' unless ($lib);
482	492	$lib = expand($lib);
483	493

519	529	undef $il;
520	530	++$has_option{sources};
521	531	}
522		my ($fi, $fl, $fil) = find_in_dir($try, $i, $l, $il);
	532	my ($fi, $fl, $fil)
	533	= find_in_dir($try, $i, $l, $il, undef, undef, $src);
523	534	if ($fi \|\| $fl \|\| $fil) {
524	535	$found_itf = $fi if (! $found_itf && $fi);
525	536	$found_lib = $fl if (! $found_lib && $fl);

540	551	}
541	552	if (! $found_itf && ! $has_option{sources} && $a{srcpath}) {
542	553	my $try = $a{srcpath};
543		($found_itf) = find_in_dir($try, $inc);
	554	($found_itf, undef, undef, $found_src)
	555	= find_in_dir($try, $inc, undef, undef, undef, undef, $src);
544	556	}
545	557	if (! $has_option{prefix}) {
546	558	my $try = $a{pkgpath};

667	679	push(@dependencies, "$a{aname}_INCDIR = $found_itf");
668	680	println "includes: $found_itf";
669	681	}
	682	if ($found_src) {
	683	$found_src = abs_path($found_src);
	684	push(@dependencies, "$a{aname}_SRCDIR = $found_src");
	685	println "sources: $found_src";
	686	}
670	687	if ($found_lib) {
671	688	$found_lib = abs_path($found_lib);
672	689	if ($a{aname} eq 'NGS' \|\| $a{aname} eq 'VDB') {

698	715	}
699	716	}
700	717
701		my ($E_BINDIR, $E_LIBDIR, $VERSION, $MAJVERS, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
702		$E_VERSION_EXEX, $E_MAJVERS_EXEX)
	718	my ($E_BINDIR, $E_LIBDIR, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
	719	$E_VERSION_EXEX, $E_MAJVERS_EXEX)
703	720	= ('' , '');
704	721
705	722	println unless ($AUTORUN);

710	727	println "configure: creating '$COMP' ($TOOLS)" unless ($AUTORUN);
711	728	open F, ">$COMP" or die "cannot open $COMP to write";
712	729	print F "$TOOLS\n";
	730	close F;
	731	}
	732
	733	if ($TOOLS =~ /gcc$/) {
	734	my $EXECMDF = File::Spec->catdir(CONFIG_OUT(), 'ld.linux.exe_cmd.sh');
	735	println "configure: creating '$EXECMDF'" unless ($AUTORUN);
	736	open F, ">$EXECMDF" or die "cannot open $EXECMDF to write";
	737	print F "EXE_CMD=\"\$LD $STATIC_LIBSTDCPP -static-libgcc\"\n";
713	738	close F;
714	739	}
715	740

772	797	# target OS
773	798	OS = $OS
774	799	OSINC = $OSINC
	800	OS_DISTRIBUTOR = $OS_DISTRIBUTOR
775	801
776	802	# prefix string for system libraries
777	803	LPFX = $LPFX

865	891	L($F, "NO_ARRAY_BOUNDS_WARNING = $NO_ARRAY_BOUNDS_WARNING");
866	892	L($F);
867	893
868		# version information
869
870		my $MAJMIN;
871
872		if ($FULL_VERSION =~ /(\d+)\.(\d+)\.(\d+)-?\w\d/) {
873		$VERSION = "$1.$2.$3";
874		$MAJMIN = "$1.$2";
875		$MAJVERS = $1;
876		} else {
877		die $VERSION;
878		}
879
880	894	print $F <<EndText;
881		# $PACKAGE_NAME and library version
882		VERSION = $VERSION
883		MAJMIN = $MAJMIN
884		MAJVERS = $MAJVERS
	895	# \$(VERSION) is defined in a separate file which is updated every release
	896	include \$(TOP)/Makefile.vers
	897
	898	empty :=
	899	space := \$(empty) \$(empty)
	900	MAJMIN = \$(subst \$(space),.,\$(wordlist 1,2,\$(subst .,\$(space),\$(VERSION))))
	901	MAJVERS = \$(firstword \$(subst .,\$(space),\$(VERSION)))
885	902
886	903	# output path
887	904	BUILD_PREFIX = $BUILD_PREFIX

971	988	L($F, 'include $(wildcard $(CLSDIR)/*.d)');
972	989	}
973	990	L($F, $_) foreach (@dependencies);
	991	L($F);
	992
	993	# pass HAVE_XML2 to build scripts
	994	L($F, 'ifeq (,$(HAVE_XML2))');
	995	L($F, ' HAVE_XML2=0');
	996	L($F, 'endif');
	997	L($F, 'CONFIGURE_FOUND_XML2=$(HAVE_XML2)');
	998	L($F, 'export CONFIGURE_FOUND_XML2');
974	999	L($F);
975	1000
976	1001	if ($OS eq 'linux' \|\| $OS eq 'mac') {

1039	1064	}
1040	1065	close $F;
1041	1066
1042		# create Makefile.config.install
1043		println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
1044		open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
1045
1046		$OPT{'javadir' } = '' unless ($OPT{'javadir' });
1047		$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
1048
1049		print $F "sub CONFIGURE {\n";
1050		print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
1051		print $F " \$_{VERSION } = '$VERSION';\n";
1052		print $F " \$_{LNG } = '$PKG{LNG}';\n";
1053		print $F " \$_{OS } = '$OS';\n";
1054		print $F " \$_{BITS } = $BITS;\n";
1055		print $F " \$_{MAJVERS } = $MAJVERS;\n";
1056		print $F " \$_{LPFX } = '$LPFX';\n";
1057		print $F " \$_{LIBX } = '$LIBX';\n";
1058		print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
1059		print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
1060		print $F " \$_{SHLX } = '$SHLX';\n";
1061		print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
1062		print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
1063		print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
1064		print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
1065		print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
1066		if ($PKG{LNG} ne 'PYTHON') {
1067		print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
1068		print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
1069		} elsif ($OPT{PYTHON_LIB_PATH}) {
1070		print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
1071		}
1072		print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
1073		print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
1074		print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
1075		print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
1076		print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
1077		print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
1078		print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
1079		print $F "\n";
1080		print $F " \@_\n";
1081		print $F "}\n";
1082		print $F "\n";
1083		print $F "1\n";
1084
1085		close $F;
	1067	# creation of Makefile.config.install is disabled, since nobody uses it now
	1068	# and I need to remove versions from prl scripts
	1069	if (0) {
	1070	# create Makefile.config.install
	1071	println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
	1072	open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
	1073
	1074	$OPT{'javadir' } = '' unless ($OPT{'javadir' });
	1075	$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
	1076
	1077	print $F "sub CONFIGURE {\n";
	1078	print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
	1079	print $F " \$_{VERSION } = '\$VERSION';\n";
	1080	print $F " \$_{LNG } = '$PKG{LNG}';\n";
	1081	print $F " \$_{OS } = '$OS';\n";
	1082	print $F " \$_{BITS } = $BITS;\n";
	1083	print $F " \$_{MAJVERS } = \$MAJVERS;\n";
	1084	print $F " \$_{LPFX } = '$LPFX';\n";
	1085	print $F " \$_{LIBX } = '$LIBX';\n";
	1086	print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
	1087	print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
	1088	print $F " \$_{SHLX } = '$SHLX';\n";
	1089	print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
	1090	print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
	1091	print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
	1092	print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
	1093	print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
	1094	if ($PKG{LNG} ne 'PYTHON') {
	1095	print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
	1096	print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
	1097	} elsif ($OPT{PYTHON_LIB_PATH}) {
	1098	print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
	1099	}
	1100	print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
	1101	print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
	1102	print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
	1103	print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
	1104	print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
	1105	print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
	1106	print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
	1107	print $F "\n";
	1108	print $F " \@_\n";
	1109	print $F "}\n";
	1110	print $F "\n";
	1111	print $F "1\n";
	1112
	1113	close $F;
	1114	}
1086	1115	}
1087	1116
1088	1117	if (! $OPT{'status'} ) {

1253	1282	}
1254	1283
1255	1284	sub find_in_dir {
1256		my ($dir, $include, $lib, $ilib, $jar, $bin) = @_;
	1285	my ($dir, $include, $lib, $ilib, $jar, $bin, $src) = @_;
1257	1286	unless (-d $dir) {
1258		# println "no" unless ($AUTORUN);
1259	1287	println "\t\tnot found $dir" if ($OPT{'debug'});
1260	1288	return;
1261	1289	}
1262		# print "\t$dir... " unless ($AUTORUN);
1263		# print "[found] " if ($OPT{'debug'});
1264		my ($found_inc, $found_lib, $found_ilib);
	1290	my ($found_inc, $found_lib, $found_ilib, $found_src);
1265	1291	if ($include) {
1266	1292	print "\tincludes... " unless ($AUTORUN);
1267	1293	if (-e "$dir/$include") {

1279	1305	}
1280	1306	}
1281	1307	if ($lib \|\| $ilib) {
1282		# print "\n\t" if ($nl && !$AUTORUN);
1283	1308	print "\tlibraries... " unless ($AUTORUN);
1284	1309	if ($lib) {
1285	1310	my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);

1371	1396	$found_lib = $try;
1372	1397	}
1373	1398	}
1374		return ($found_inc, $found_lib, $found_ilib);
	1399	if ($src) {
	1400	print "\tsrc... " unless ($AUTORUN);
	1401	my $try = "$dir/$src";
	1402	if (-e "$try") {
	1403	println $dir unless ($AUTORUN);
	1404	$found_src = $dir;
	1405	}
	1406	}
	1407	return ($found_inc, $found_lib, $found_ilib, $found_src);
1375	1408	}
1376	1409
1377	1410	sub reverse_build {

1409	1442	check_compiler('O', '-Wno-array-bounds');
1410	1443	}
1411	1444
	1445	sub check_static_libstdcpp {
	1446	my $option = '-static-libstdc++';
	1447	my $save = $TOOLS;
	1448	$TOOLS = $CPP;
	1449	$_ = check_compiler('O', $option);
	1450	$TOOLS = $save;
	1451	$_ ? $option : ''
	1452	}
	1453
1412	1454	sub find_lib {
1413	1455	check_compiler('L', @_);
1414	1456	}

1420	1462	if ($t eq 'L') {
1421	1463	print "checking for $n library... ";
1422	1464	} elsif ($t eq 'O') {
1423		if ($tool && $tool =~ /gcc$/) {
	1465	if ($tool && ($tool =~ /gcc$/ \|\| $tool =~ /g\+\+$/)) {
1424	1466	print "checking whether $tool accepts $n... ";
1425	1467	} else {
1426	1468	return;

1451	1493	$library = '-lmagic';
1452	1494	$log = '#include <magic.h> \n int main() { magic_open (0); }\n'
1453	1495	} elsif ($n eq 'xml2') {
1454		$library = '-lxml2';
	1496	$library = '-lxml2';
	1497	$library .= ' -liconv' if ($OS eq 'mac');
1455	1498	$log = '#include <libxml/xmlreader.h>\n' .
1456	1499	'int main() { xmlInitParser ( ); }\n'
1457	1500	} else {

1503	1546	die "No PACKAGE_NAME" unless PACKAGE_NAME();
1504	1547	die "No PACKAGE_NAMW" unless PACKAGE_NAMW();
1505	1548	die "No PACKAGE_TYPE" unless PACKAGE_TYPE();
1506		die "No VERSION" unless VERSION();
1507	1549
1508	1550	my %PKG = PKG();
1509	1551

+0

-1

ngs-java/setup/package.prl less more

0	0	################################################################################
1	1	sub PACKAGE { 'ngs-java' }
2		sub VERSION { '1.2.4' }
3	2	sub PACKAGE_TYPE { 'J' }
4	3	sub PACKAGE_NAME { 'NGS-JAVA' }
5	4	sub PACKAGE_NAMW { 'NGS_JAVA' }

+1

-0

ngs-python/.gitignore less more

0	0	*.pyc
1	1	/build
	2	/ld.linux.exe_cmd.sh
2	3	/Makefile.userconfig
3	4	/Makefile.config*
4	5	/reconfigure

+26

-0

ngs-python/Makefile.vers less more

	0	# ===========================================================================
	1	#
	2	# PUBLIC DOMAIN NOTICE
	3	# National Center for Biotechnology Information
	4	#
	5	# This software/database is a "United States Government Work" under the
	6	# terms of the United States Copyright Act. It was written as part of
	7	# the author's official duties as a United States Government employee and
	8	# thus cannot be copyrighted. This software/database is freely available
	9	# to the public for use. The National Library of Medicine and the U.S.
	10	# Government have not placed any restriction on its use or reproduction.
	11	#
	12	# Although all reasonable efforts have been taken to ensure the accuracy
	13	# and reliability of the software and data, the NLM and the U.S.
	14	# Government do not and cannot warrant the performance or results that
	15	# may be obtained by using this software or data. The NLM and the U.S.
	16	# Government disclaim all warranties, express or implied, including
	17	# warranties of performance, merchantability or fitness for any particular
	18	# purpose.
	19	#
	20	# Please cite the author in any work or product based on this material.
	21	#
	22	# ===========================================================================
	23
	24	# NGS-PYTHON and library version
	25	VERSION = 1.2.5

+123

-81

ngs-python/setup/konfigure.perl less more

202	202	exit 1;
203	203	}
204	204
	205	my $OS_DISTRIBUTOR = '';
	206	if ($OS eq 'linux') {
	207	print "checking OS distributor... " unless ($AUTORUN);
	208	$OS_DISTRIBUTOR = `lsb_release -si 2> /dev/null`;
	209	chomp $OS_DISTRIBUTOR;
	210	println $OS_DISTRIBUTOR unless ($AUTORUN);
	211	}
	212
205	213	print "checking machine architecture... " unless ($AUTORUN);
206	214	println $MARCH unless ($AUTORUN);
207	215	unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /i?86/i) {

282	290
283	291	my $TOOLS = "";
284	292	$TOOLS = "jdk" if ($PKG{LNG} eq 'JAVA');
285
286		print "checking $PACKAGE_NAME version... " unless ($AUTORUN);
287		my $FULL_VERSION = VERSION();
288		println $FULL_VERSION unless ($AUTORUN);
289	293
290	294	# determine architecture
291	295

423	427	$NO_ARRAY_BOUNDS_WARNING = '-Wno-array-bounds';
424	428	}
425	429
	430	my $STATIC_LIBSTDCPP = '';
	431	if ($TOOLS =~ /gcc$/) {
	432	$STATIC_LIBSTDCPP = check_static_libstdcpp();
	433	}
	434
426	435	my @dependencies;
427	436
428	437	my %DEPEND_OPTIONS;

463	472	$href->{locbldpath} = expand($href->{locbldpath}) if ($href->{locbldpath});
464	473
465	474	# found directories
466		my ($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar);
	475	my
	476	($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar, $found_src);
467	477
468	478	my %a = %$href;
469	479	next if ($a{option} && $DEPEND_OPTIONS{$a{option}});

476	486	my $need_itf = ! ($a{type} =~ /D/ \|\| $a{type} =~ /E/ \|\| $a{type} =~ /J/);
477	487	my $need_jar = $a{type} =~ /J/;
478	488
479		my ($bin, $inc, $lib, $ilib)
480		= ($a{bin}, $a{include}, $a{lib}); # file names to check
	489	my ($bin, $inc, $lib, $ilib, $src)
	490	= ($a{bin}, $a{include}, $a{lib}, undef, $a{src}); # file names to check
481	491	$lib = '' unless ($lib);
482	492	$lib = expand($lib);
483	493

519	529	undef $il;
520	530	++$has_option{sources};
521	531	}
522		my ($fi, $fl, $fil) = find_in_dir($try, $i, $l, $il);
	532	my ($fi, $fl, $fil)
	533	= find_in_dir($try, $i, $l, $il, undef, undef, $src);
523	534	if ($fi \|\| $fl \|\| $fil) {
524	535	$found_itf = $fi if (! $found_itf && $fi);
525	536	$found_lib = $fl if (! $found_lib && $fl);

540	551	}
541	552	if (! $found_itf && ! $has_option{sources} && $a{srcpath}) {
542	553	my $try = $a{srcpath};
543		($found_itf) = find_in_dir($try, $inc);
	554	($found_itf, undef, undef, $found_src)
	555	= find_in_dir($try, $inc, undef, undef, undef, undef, $src);
544	556	}
545	557	if (! $has_option{prefix}) {
546	558	my $try = $a{pkgpath};

667	679	push(@dependencies, "$a{aname}_INCDIR = $found_itf");
668	680	println "includes: $found_itf";
669	681	}
	682	if ($found_src) {
	683	$found_src = abs_path($found_src);
	684	push(@dependencies, "$a{aname}_SRCDIR = $found_src");
	685	println "sources: $found_src";
	686	}
670	687	if ($found_lib) {
671	688	$found_lib = abs_path($found_lib);
672	689	if ($a{aname} eq 'NGS' \|\| $a{aname} eq 'VDB') {

698	715	}
699	716	}
700	717
701		my ($E_BINDIR, $E_LIBDIR, $VERSION, $MAJVERS, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
702		$E_VERSION_EXEX, $E_MAJVERS_EXEX)
	718	my ($E_BINDIR, $E_LIBDIR, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
	719	$E_VERSION_EXEX, $E_MAJVERS_EXEX)
703	720	= ('' , '');
704	721
705	722	println unless ($AUTORUN);

710	727	println "configure: creating '$COMP' ($TOOLS)" unless ($AUTORUN);
711	728	open F, ">$COMP" or die "cannot open $COMP to write";
712	729	print F "$TOOLS\n";
	730	close F;
	731	}
	732
	733	if ($TOOLS =~ /gcc$/) {
	734	my $EXECMDF = File::Spec->catdir(CONFIG_OUT(), 'ld.linux.exe_cmd.sh');
	735	println "configure: creating '$EXECMDF'" unless ($AUTORUN);
	736	open F, ">$EXECMDF" or die "cannot open $EXECMDF to write";
	737	print F "EXE_CMD=\"\$LD $STATIC_LIBSTDCPP -static-libgcc\"\n";
713	738	close F;
714	739	}
715	740

772	797	# target OS
773	798	OS = $OS
774	799	OSINC = $OSINC
	800	OS_DISTRIBUTOR = $OS_DISTRIBUTOR
775	801
776	802	# prefix string for system libraries
777	803	LPFX = $LPFX

865	891	L($F, "NO_ARRAY_BOUNDS_WARNING = $NO_ARRAY_BOUNDS_WARNING");
866	892	L($F);
867	893
868		# version information
869
870		my $MAJMIN;
871
872		if ($FULL_VERSION =~ /(\d+)\.(\d+)\.(\d+)-?\w\d/) {
873		$VERSION = "$1.$2.$3";
874		$MAJMIN = "$1.$2";
875		$MAJVERS = $1;
876		} else {
877		die $VERSION;
878		}
879
880	894	print $F <<EndText;
881		# $PACKAGE_NAME and library version
882		VERSION = $VERSION
883		MAJMIN = $MAJMIN
884		MAJVERS = $MAJVERS
	895	# \$(VERSION) is defined in a separate file which is updated every release
	896	include \$(TOP)/Makefile.vers
	897
	898	empty :=
	899	space := \$(empty) \$(empty)
	900	MAJMIN = \$(subst \$(space),.,\$(wordlist 1,2,\$(subst .,\$(space),\$(VERSION))))
	901	MAJVERS = \$(firstword \$(subst .,\$(space),\$(VERSION)))
885	902
886	903	# output path
887	904	BUILD_PREFIX = $BUILD_PREFIX

971	988	L($F, 'include $(wildcard $(CLSDIR)/*.d)');
972	989	}
973	990	L($F, $_) foreach (@dependencies);
	991	L($F);
	992
	993	# pass HAVE_XML2 to build scripts
	994	L($F, 'ifeq (,$(HAVE_XML2))');
	995	L($F, ' HAVE_XML2=0');
	996	L($F, 'endif');
	997	L($F, 'CONFIGURE_FOUND_XML2=$(HAVE_XML2)');
	998	L($F, 'export CONFIGURE_FOUND_XML2');
974	999	L($F);
975	1000
976	1001	if ($OS eq 'linux' \|\| $OS eq 'mac') {

1039	1064	}
1040	1065	close $F;
1041	1066
1042		# create Makefile.config.install
1043		println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
1044		open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
1045
1046		$OPT{'javadir' } = '' unless ($OPT{'javadir' });
1047		$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
1048
1049		print $F "sub CONFIGURE {\n";
1050		print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
1051		print $F " \$_{VERSION } = '$VERSION';\n";
1052		print $F " \$_{LNG } = '$PKG{LNG}';\n";
1053		print $F " \$_{OS } = '$OS';\n";
1054		print $F " \$_{BITS } = $BITS;\n";
1055		print $F " \$_{MAJVERS } = $MAJVERS;\n";
1056		print $F " \$_{LPFX } = '$LPFX';\n";
1057		print $F " \$_{LIBX } = '$LIBX';\n";
1058		print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
1059		print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
1060		print $F " \$_{SHLX } = '$SHLX';\n";
1061		print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
1062		print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
1063		print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
1064		print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
1065		print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
1066		if ($PKG{LNG} ne 'PYTHON') {
1067		print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
1068		print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
1069		} elsif ($OPT{PYTHON_LIB_PATH}) {
1070		print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
1071		}
1072		print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
1073		print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
1074		print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
1075		print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
1076		print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
1077		print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
1078		print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
1079		print $F "\n";
1080		print $F " \@_\n";
1081		print $F "}\n";
1082		print $F "\n";
1083		print $F "1\n";
1084
1085		close $F;
	1067	# creation of Makefile.config.install is disabled, since nobody uses it now
	1068	# and I need to remove versions from prl scripts
	1069	if (0) {
	1070	# create Makefile.config.install
	1071	println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
	1072	open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
	1073
	1074	$OPT{'javadir' } = '' unless ($OPT{'javadir' });
	1075	$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
	1076
	1077	print $F "sub CONFIGURE {\n";
	1078	print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
	1079	print $F " \$_{VERSION } = '\$VERSION';\n";
	1080	print $F " \$_{LNG } = '$PKG{LNG}';\n";
	1081	print $F " \$_{OS } = '$OS';\n";
	1082	print $F " \$_{BITS } = $BITS;\n";
	1083	print $F " \$_{MAJVERS } = \$MAJVERS;\n";
	1084	print $F " \$_{LPFX } = '$LPFX';\n";
	1085	print $F " \$_{LIBX } = '$LIBX';\n";
	1086	print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
	1087	print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
	1088	print $F " \$_{SHLX } = '$SHLX';\n";
	1089	print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
	1090	print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
	1091	print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
	1092	print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
	1093	print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
	1094	if ($PKG{LNG} ne 'PYTHON') {
	1095	print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
	1096	print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
	1097	} elsif ($OPT{PYTHON_LIB_PATH}) {
	1098	print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
	1099	}
	1100	print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
	1101	print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
	1102	print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
	1103	print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
	1104	print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
	1105	print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
	1106	print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
	1107	print $F "\n";
	1108	print $F " \@_\n";
	1109	print $F "}\n";
	1110	print $F "\n";
	1111	print $F "1\n";
	1112
	1113	close $F;
	1114	}
1086	1115	}
1087	1116
1088	1117	if (! $OPT{'status'} ) {

1253	1282	}
1254	1283
1255	1284	sub find_in_dir {
1256		my ($dir, $include, $lib, $ilib, $jar, $bin) = @_;
	1285	my ($dir, $include, $lib, $ilib, $jar, $bin, $src) = @_;
1257	1286	unless (-d $dir) {
1258		# println "no" unless ($AUTORUN);
1259	1287	println "\t\tnot found $dir" if ($OPT{'debug'});
1260	1288	return;
1261	1289	}
1262		# print "\t$dir... " unless ($AUTORUN);
1263		# print "[found] " if ($OPT{'debug'});
1264		my ($found_inc, $found_lib, $found_ilib);
	1290	my ($found_inc, $found_lib, $found_ilib, $found_src);
1265	1291	if ($include) {
1266	1292	print "\tincludes... " unless ($AUTORUN);
1267	1293	if (-e "$dir/$include") {

1279	1305	}
1280	1306	}
1281	1307	if ($lib \|\| $ilib) {
1282		# print "\n\t" if ($nl && !$AUTORUN);
1283	1308	print "\tlibraries... " unless ($AUTORUN);
1284	1309	if ($lib) {
1285	1310	my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);

1371	1396	$found_lib = $try;
1372	1397	}
1373	1398	}
1374		return ($found_inc, $found_lib, $found_ilib);
	1399	if ($src) {
	1400	print "\tsrc... " unless ($AUTORUN);
	1401	my $try = "$dir/$src";
	1402	if (-e "$try") {
	1403	println $dir unless ($AUTORUN);
	1404	$found_src = $dir;
	1405	}
	1406	}
	1407	return ($found_inc, $found_lib, $found_ilib, $found_src);
1375	1408	}
1376	1409
1377	1410	sub reverse_build {

1409	1442	check_compiler('O', '-Wno-array-bounds');
1410	1443	}
1411	1444
	1445	sub check_static_libstdcpp {
	1446	my $option = '-static-libstdc++';
	1447	my $save = $TOOLS;
	1448	$TOOLS = $CPP;
	1449	$_ = check_compiler('O', $option);
	1450	$TOOLS = $save;
	1451	$_ ? $option : ''
	1452	}
	1453
1412	1454	sub find_lib {
1413	1455	check_compiler('L', @_);
1414	1456	}

1420	1462	if ($t eq 'L') {
1421	1463	print "checking for $n library... ";
1422	1464	} elsif ($t eq 'O') {
1423		if ($tool && $tool =~ /gcc$/) {
	1465	if ($tool && ($tool =~ /gcc$/ \|\| $tool =~ /g\+\+$/)) {
1424	1466	print "checking whether $tool accepts $n... ";
1425	1467	} else {
1426	1468	return;

1451	1493	$library = '-lmagic';
1452	1494	$log = '#include <magic.h> \n int main() { magic_open (0); }\n'
1453	1495	} elsif ($n eq 'xml2') {
1454		$library = '-lxml2';
	1496	$library = '-lxml2';
	1497	$library .= ' -liconv' if ($OS eq 'mac');
1455	1498	$log = '#include <libxml/xmlreader.h>\n' .
1456	1499	'int main() { xmlInitParser ( ); }\n'
1457	1500	} else {

1503	1546	die "No PACKAGE_NAME" unless PACKAGE_NAME();
1504	1547	die "No PACKAGE_NAMW" unless PACKAGE_NAMW();
1505	1548	die "No PACKAGE_TYPE" unless PACKAGE_TYPE();
1506		die "No VERSION" unless VERSION();
1507	1549
1508	1550	my %PKG = PKG();
1509	1551

+0

-1

ngs-python/setup/package.prl less more

0	0	################################################################################
1	1	sub PACKAGE { 'ngs-python' }
2		sub VERSION { '1.2.4' }
3	2	sub PACKAGE_TYPE { 'P' }
4	3	sub PACKAGE_NAME { 'NGS-PYTHON' }
5	4	sub PACKAGE_NAMW { 'NGS_PYTHON' }

+1

-0

ngs-sdk/.gitignore less more

0	0	*.o
	1	/ld.linux.exe_cmd.sh
1	2	/Makefile.config*
2	3	/Makefile.userconfig
3	4	/reconfigure

+1

-1

ngs-sdk/Makefile less more

36	36
37	37	include $(CURDIR)/Makefile.rules
38	38
39		sdk-libs: Makefile.config
	39	sdk-libs: $(SUBDIRS) Makefile.config
40	40	@ $(MAKE) -f Makefile.libs
41	41
42	42	sdk-libs_cln: Makefile.config

+26

-0

ngs-sdk/Makefile.vers less more

	0	# ===========================================================================
	1	#
	2	# PUBLIC DOMAIN NOTICE
	3	# National Center for Biotechnology Information
	4	#
	5	# This software/database is a "United States Government Work" under the
	6	# terms of the United States Copyright Act. It was written as part of
	7	# the author's official duties as a United States Government employee and
	8	# thus cannot be copyrighted. This software/database is freely available
	9	# to the public for use. The National Library of Medicine and the U.S.
	10	# Government have not placed any restriction on its use or reproduction.
	11	#
	12	# Although all reasonable efforts have been taken to ensure the accuracy
	13	# and reliability of the software and data, the NLM and the U.S.
	14	# Government do not and cannot warrant the performance or results that
	15	# may be obtained by using this software or data. The NLM and the U.S.
	16	# Government disclaim all warranties, express or implied, including
	17	# warranties of performance, merchantability or fitness for any particular
	18	# purpose.
	19	#
	20	# Please cite the author in any work or product based on this material.
	21	#
	22	# ===========================================================================
	23
	24	# NGS-SDK and library version
	25	VERSION = 1.2.5

+1

-1

ngs-sdk/dispatch/version.h less more

0		#define NGS_SDK_VERSION "1.2.4"
	0	#define NGS_SDK_VERSION "1.2.5"

+8

-2

ngs-sdk/language/java/jni_String.cpp less more

122	122	at least when it comes to UTF-8 character sets... */
123	123
124	124	/* an awful, but effective, test to see if the string
125		is already NUL terminated. */
	125	is already NUL terminated:
	126	1. we assume that buffer SIZE is aligned to 12 bits
	127	2. we check if string size is less than buffer size,
	128	i.e. if data[size] belongs buffer of not
	129	3. if data[size] belongs to the buffer,
	130	we can check if string is followed by NULL byte */
126	131	if ( ( ( ( size_t ) & data [ size ] ) & 0xFFF ) != 0 )
127	132	{
128	133	/* we can read this address without fear of a seg-fault.
129		if it's NUL, then we can send the string in directly. */
	134	if it's NUL, then we can send the string in directly.
	135	NB: valgrind may complain about this line, but it is okay */
130	136	if ( data [ size ] == 0 )
131	137	return jenv -> NewStringUTF ( data );
132	138	}

+123

-80

ngs-sdk/setup/konfigure.perl less more

202	202	exit 1;
203	203	}
204	204
	205	my $OS_DISTRIBUTOR = '';
	206	if ($OS eq 'linux') {
	207	print "checking OS distributor... " unless ($AUTORUN);
	208	$OS_DISTRIBUTOR = `lsb_release -si 2> /dev/null`;
	209	chomp $OS_DISTRIBUTOR;
	210	println $OS_DISTRIBUTOR unless ($AUTORUN);
	211	}
	212
205	213	print "checking machine architecture... " unless ($AUTORUN);
206	214	println $MARCH unless ($AUTORUN);
207	215	unless ($MARCH =~ /x86_64/i \|\| $MARCH =~ /i?86/i) {

282	290
283	291	my $TOOLS = "";
284	292	$TOOLS = "jdk" if ($PKG{LNG} eq 'JAVA');
285
286		print "checking $PACKAGE_NAME version... " unless ($AUTORUN);
287		my $FULL_VERSION = VERSION();
288		println $FULL_VERSION unless ($AUTORUN);
289	293
290	294	# determine architecture
291	295

423	427	$NO_ARRAY_BOUNDS_WARNING = '-Wno-array-bounds';
424	428	}
425	429
	430	my $STATIC_LIBSTDCPP = '';
	431	if ($TOOLS =~ /gcc$/) {
	432	$STATIC_LIBSTDCPP = check_static_libstdcpp();
	433	}
	434
426	435	my @dependencies;
427	436
428	437	my %DEPEND_OPTIONS;

463	472	$href->{locbldpath} = expand($href->{locbldpath}) if ($href->{locbldpath});
464	473
465	474	# found directories
466		my ($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar);
	475	my
	476	($found_itf, $found_bin, $found_lib, $found_ilib, $found_jar, $found_src);
467	477
468	478	my %a = %$href;
469	479	next if ($a{option} && $DEPEND_OPTIONS{$a{option}});

476	486	my $need_itf = ! ($a{type} =~ /D/ \|\| $a{type} =~ /E/ \|\| $a{type} =~ /J/);
477	487	my $need_jar = $a{type} =~ /J/;
478	488
479		my ($bin, $inc, $lib, $ilib)
480		= ($a{bin}, $a{include}, $a{lib}); # file names to check
	489	my ($bin, $inc, $lib, $ilib, $src)
	490	= ($a{bin}, $a{include}, $a{lib}, undef, $a{src}); # file names to check
481	491	$lib = '' unless ($lib);
482	492	$lib = expand($lib);
483	493

519	529	undef $il;
520	530	++$has_option{sources};
521	531	}
522		my ($fi, $fl, $fil) = find_in_dir($try, $i, $l, $il);
	532	my ($fi, $fl, $fil)
	533	= find_in_dir($try, $i, $l, $il, undef, undef, $src);
523	534	if ($fi \|\| $fl \|\| $fil) {
524	535	$found_itf = $fi if (! $found_itf && $fi);
525	536	$found_lib = $fl if (! $found_lib && $fl);

540	551	}
541	552	if (! $found_itf && ! $has_option{sources} && $a{srcpath}) {
542	553	my $try = $a{srcpath};
543		($found_itf) = find_in_dir($try, $inc);
	554	($found_itf, undef, undef, $found_src)
	555	= find_in_dir($try, $inc, undef, undef, undef, undef, $src);
544	556	}
545	557	if (! $has_option{prefix}) {
546	558	my $try = $a{pkgpath};

667	679	push(@dependencies, "$a{aname}_INCDIR = $found_itf");
668	680	println "includes: $found_itf";
669	681	}
	682	if ($found_src) {
	683	$found_src = abs_path($found_src);
	684	push(@dependencies, "$a{aname}_SRCDIR = $found_src");
	685	println "sources: $found_src";
	686	}
670	687	if ($found_lib) {
671	688	$found_lib = abs_path($found_lib);
672	689	if ($a{aname} eq 'NGS' \|\| $a{aname} eq 'VDB') {

698	715	}
699	716	}
700	717
701		my ($E_BINDIR, $E_LIBDIR, $VERSION, $MAJVERS, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
702		$E_VERSION_EXEX, $E_MAJVERS_EXEX)
	718	my ($E_BINDIR, $E_LIBDIR, $E_VERSION_LIBX, $E_MAJVERS_LIBX,
	719	$E_VERSION_EXEX, $E_MAJVERS_EXEX)
703	720	= ('' , '');
704	721
705	722	println unless ($AUTORUN);

710	727	println "configure: creating '$COMP' ($TOOLS)" unless ($AUTORUN);
711	728	open F, ">$COMP" or die "cannot open $COMP to write";
712	729	print F "$TOOLS\n";
	730	close F;
	731	}
	732
	733	if ($TOOLS =~ /gcc$/) {
	734	my $EXECMDF = File::Spec->catdir(CONFIG_OUT(), 'ld.linux.exe_cmd.sh');
	735	println "configure: creating '$EXECMDF'" unless ($AUTORUN);
	736	open F, ">$EXECMDF" or die "cannot open $EXECMDF to write";
	737	print F "EXE_CMD=\"\$LD $STATIC_LIBSTDCPP -static-libgcc\"\n";
713	738	close F;
714	739	}
715	740

772	797	# target OS
773	798	OS = $OS
774	799	OSINC = $OSINC
	800	OS_DISTRIBUTOR = $OS_DISTRIBUTOR
775	801
776	802	# prefix string for system libraries
777	803	LPFX = $LPFX

865	891	L($F, "NO_ARRAY_BOUNDS_WARNING = $NO_ARRAY_BOUNDS_WARNING");
866	892	L($F);
867	893
868		# version information
869
870		my $MAJMIN;
871
872		if ($FULL_VERSION =~ /(\d+)\.(\d+)\.(\d+)-?\w\d/) {
873		$VERSION = "$1.$2.$3";
874		$MAJMIN = "$1.$2";
875		$MAJVERS = $1;
876		} else {
877		die $VERSION;
878		}
879
880	894	print $F <<EndText;
881	895	# $PACKAGE_NAME and library version
882		VERSION = $VERSION
883		MAJMIN = $MAJMIN
884		MAJVERS = $MAJVERS
	896	# \$(VERSION) is defined in a separate file which is updated every release
	897	include \$(TOP)/Makefile.vers
	898
	899	empty :=
	900	space := \$(empty) \$(empty)
	901	MAJMIN = \$(subst \$(space),.,\$(wordlist 1,2,\$(subst .,\$(space),\$(VERSION))))
	902	MAJVERS = \$(firstword \$(subst .,\$(space),\$(VERSION)))
885	903
886	904	# output path
887	905	BUILD_PREFIX = $BUILD_PREFIX

971	989	L($F, 'include $(wildcard $(CLSDIR)/*.d)');
972	990	}
973	991	L($F, $_) foreach (@dependencies);
	992	L($F);
	993
	994	# pass HAVE_XML2 to build scripts
	995	L($F, 'ifeq (,$(HAVE_XML2))');
	996	L($F, ' HAVE_XML2=0');
	997	L($F, 'endif');
	998	L($F, 'CONFIGURE_FOUND_XML2=$(HAVE_XML2)');
	999	L($F, 'export CONFIGURE_FOUND_XML2');
974	1000	L($F);
975	1001
976	1002	if ($OS eq 'linux' \|\| $OS eq 'mac') {

1039	1065	}
1040	1066	close $F;
1041	1067
1042		# create Makefile.config.install
1043		println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
1044		open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
1045
1046		$OPT{'javadir' } = '' unless ($OPT{'javadir' });
1047		$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
1048
1049		print $F "sub CONFIGURE {\n";
1050		print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
1051		print $F " \$_{VERSION } = '$VERSION';\n";
1052		print $F " \$_{LNG } = '$PKG{LNG}';\n";
1053		print $F " \$_{OS } = '$OS';\n";
1054		print $F " \$_{BITS } = $BITS;\n";
1055		print $F " \$_{MAJVERS } = $MAJVERS;\n";
1056		print $F " \$_{LPFX } = '$LPFX';\n";
1057		print $F " \$_{LIBX } = '$LIBX';\n";
1058		print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
1059		print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
1060		print $F " \$_{SHLX } = '$SHLX';\n";
1061		print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
1062		print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
1063		print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
1064		print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
1065		print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
1066		if ($PKG{LNG} ne 'PYTHON') {
1067		print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
1068		print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
1069		} elsif ($OPT{PYTHON_LIB_PATH}) {
1070		print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
1071		}
1072		print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
1073		print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
1074		print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
1075		print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
1076		print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
1077		print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
1078		print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
1079		print $F "\n";
1080		print $F " \@_\n";
1081		print $F "}\n";
1082		print $F "\n";
1083		print $F "1\n";
1084
1085		close $F;
	1068	# creation of Makefile.config.install is disabled, since nobody uses it now
	1069	# and I need to remove versions from prl scripts
	1070	if (0) {
	1071	# create Makefile.config.install
	1072	println "configure: creating '$INS_MAKEFILE'" unless ($AUTORUN);
	1073	open $F, ">$INS_MAKEFILE" or die "cannot open $INS_MAKEFILE to write";
	1074
	1075	$OPT{'javadir' } = '' unless ($OPT{'javadir' });
	1076	$OPT{'sharedir'} = '' unless ($OPT{'sharedir'});
	1077
	1078	print $F "sub CONFIGURE {\n";
	1079	print $F " \$_{PACKAGE_NAME } = '$PACKAGE_NAME';\n";
	1080	print $F " \$_{VERSION } = '\$VERSION';\n";
	1081	print $F " \$_{LNG } = '$PKG{LNG}';\n";
	1082	print $F " \$_{OS } = '$OS';\n";
	1083	print $F " \$_{BITS } = $BITS;\n";
	1084	print $F " \$_{MAJVERS } = \$MAJVERS;\n";
	1085	print $F " \$_{LPFX } = '$LPFX';\n";
	1086	print $F " \$_{LIBX } = '$LIBX';\n";
	1087	print $F " \$_{MAJVERS_LIBX } = '" . expand($E_MAJVERS_LIBX) . "';\n";
	1088	print $F " \$_{VERSION_LIBX } = '" . expand($E_VERSION_LIBX) . "';\n";
	1089	print $F " \$_{SHLX } = '$SHLX';\n";
	1090	print $F " \$_{MAJVERS_SHLX } = '" . expand($E_MAJVERS_SHLX) . "';\n";
	1091	print $F " \$_{VERSION_SHLX } = '" . expand($E_VERSION_SHLX) . "';\n";
	1092	print $F " \$_{VERSION_EXEX } = '" . expand($E_VERSION_EXEX) . "';\n";
	1093	print $F " \$_{MAJVERS_EXEX } = '" . expand($E_MAJVERS_EXEX) . "';\n";
	1094	print $F " \$_{INCDIR } = '" . expand("$Bin/.." ) . "';\n";
	1095	if ($PKG{LNG} ne 'PYTHON') {
	1096	print $F " \$_{BINDIR$BITS} = '" . expand($E_BINDIR ) . "';\n";
	1097	print $F " \$_{LIBDIR$BITS} = '" . expand($E_LIBDIR ) . "';\n";
	1098	} elsif ($OPT{PYTHON_LIB_PATH}) {
	1099	print $F " \$_{LIBDIR$BITS} = '$OPT{PYTHON_LIB_PATH}';\n";
	1100	}
	1101	print $F " \$_{OTHER_PREFIX } = '$PKG{UPATH}';\n";
	1102	print $F " \$_{PREFIX } = '$OPT{'prefix'}';\n";
	1103	print $F " \$_{INST_INCDIR } = '$OPT{'includedir'}';\n";
	1104	print $F " \$_{INST_BINDIR } = '$OPT{'bindir'}';\n";
	1105	print $F " \$_{INST_LIBDIR } = '$OPT{'libdir'}';\n";
	1106	print $F " \$_{INST_JARDIR } = '$OPT{'javadir'}';\n";
	1107	print $F " \$_{INST_SHAREDIR} = '$OPT{'sharedir'}';\n";
	1108	print $F "\n";
	1109	print $F " \@_\n";
	1110	print $F "}\n";
	1111	print $F "\n";
	1112	print $F "1\n";
	1113
	1114	close $F;
	1115	}
1086	1116	}
1087	1117
1088	1118	if (! $OPT{'status'} ) {

1253	1283	}
1254	1284
1255	1285	sub find_in_dir {
1256		my ($dir, $include, $lib, $ilib, $jar, $bin) = @_;
	1286	my ($dir, $include, $lib, $ilib, $jar, $bin, $src) = @_;
1257	1287	unless (-d $dir) {
1258		# println "no" unless ($AUTORUN);
1259	1288	println "\t\tnot found $dir" if ($OPT{'debug'});
1260	1289	return;
1261	1290	}
1262		# print "\t$dir... " unless ($AUTORUN);
1263		# print "[found] " if ($OPT{'debug'});
1264		my ($found_inc, $found_lib, $found_ilib);
	1291	my ($found_inc, $found_lib, $found_ilib, $found_src);
1265	1292	if ($include) {
1266	1293	print "\tincludes... " unless ($AUTORUN);
1267	1294	if (-e "$dir/$include") {

1279	1306	}
1280	1307	}
1281	1308	if ($lib \|\| $ilib) {
1282		# print "\n\t" if ($nl && !$AUTORUN);
1283	1309	print "\tlibraries... " unless ($AUTORUN);
1284	1310	if ($lib) {
1285	1311	my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);

1371	1397	$found_lib = $try;
1372	1398	}
1373	1399	}
1374		return ($found_inc, $found_lib, $found_ilib);
	1400	if ($src) {
	1401	print "\tsrc... " unless ($AUTORUN);
	1402	my $try = "$dir/$src";
	1403	if (-e "$try") {
	1404	println $dir unless ($AUTORUN);
	1405	$found_src = $dir;
	1406	}
	1407	}
	1408	return ($found_inc, $found_lib, $found_ilib, $found_src);
1375	1409	}
1376	1410
1377	1411	sub reverse_build {

1409	1443	check_compiler('O', '-Wno-array-bounds');
1410	1444	}
1411	1445
	1446	sub check_static_libstdcpp {
	1447	my $option = '-static-libstdc++';
	1448	my $save = $TOOLS;
	1449	$TOOLS = $CPP;
	1450	$_ = check_compiler('O', $option);
	1451	$TOOLS = $save;
	1452	$_ ? $option : ''
	1453	}
	1454
1412	1455	sub find_lib {
1413	1456	check_compiler('L', @_);
1414	1457	}

1420	1463	if ($t eq 'L') {
1421	1464	print "checking for $n library... ";
1422	1465	} elsif ($t eq 'O') {
1423		if ($tool && $tool =~ /gcc$/) {
	1466	if ($tool && ($tool =~ /gcc$/ \|\| $tool =~ /g\+\+$/)) {
1424	1467	print "checking whether $tool accepts $n... ";
1425	1468	} else {
1426	1469	return;

1451	1494	$library = '-lmagic';
1452	1495	$log = '#include <magic.h> \n int main() { magic_open (0); }\n'
1453	1496	} elsif ($n eq 'xml2') {
1454		$library = '-lxml2';
	1497	$library = '-lxml2';
	1498	$library .= ' -liconv' if ($OS eq 'mac');
1455	1499	$log = '#include <libxml/xmlreader.h>\n' .
1456	1500	'int main() { xmlInitParser ( ); }\n'
1457	1501	} else {

1503	1547	die "No PACKAGE_NAME" unless PACKAGE_NAME();
1504	1548	die "No PACKAGE_NAMW" unless PACKAGE_NAMW();
1505	1549	die "No PACKAGE_TYPE" unless PACKAGE_TYPE();
1506		die "No VERSION" unless VERSION();
1507	1550
1508	1551	my %PKG = PKG();
1509	1552

+0

-1

ngs-sdk/setup/package.prl less more

0	0	################################################################################
1	1	sub PACKAGE { 'ngs-sdk' }
2		sub VERSION { '1.2.4' }
3	2	sub PACKAGE_TYPE { 'L' }
4	3	sub PACKAGE_NAME { 'NGS-SDK' }
5	4	sub PACKAGE_NAMW { 'NGS' }

0	0	# NCBI External Developer Release:
	1
	2	## NGS SDK 1.2.5
	3	July 12, 2016
	4
	5	blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
	6	htsjdk: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK
	7	kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME
	8	ngs, search, sra-search: sra-search was modified to support multiple threads.
	9	ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored
	10	ngs-engine: Added support for blob-by-blob access to SEQUENCE table
	11	ngs-engine: removed a potential memory leak in NGS_CursorMake()
	12	ngs: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs
	13	ngs: now supports parallel compilation with "make -j N"
	14	vfs: environment variable VDB_PWFILE is no longer used
	15
1	16
2	17	## NGS SDK 1.2.4
3	18	May 25, 2016
4	19
5		build: MSVS 2013 toolset (12.0) is now supported across all repositories
6		doc, ngs: updated javadoc to include throws and other missing tags
7		examples, ngs: added DumpReferenceFASTA.py example
8		htsjdk: added code to HTS-JDK to avoid involving NGS unless we are sure that it is being requested
9		ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments
10		ngs, test: ngs-python: fixed bug in String processing for Python 3.*
11		ngs-engine: ncbi-ngs engine was updated: fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
12		ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries
13		ngs: Python code will check for the latest version of the libraries and update if newer ones are available
14		ngs: check for the latest version of the libraries and update if newer ones are available
15		ngs: simplified ngs-python bindings
	20	build: MSVS 2013 toolset (12.0) is now supported across all repositories
	21	doc, ngs: updated javadoc to include throws and other missing tags
	22	examples, ngs: added DumpReferenceFASTA.py example
	23	htsjdk: added code to HTS-JDK to avoid involving NGS unless we are sure that it is being requested
	24	ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments
	25	ngs, test, ngs-python: fixed bug in String processing for Python 3.x
	26	ngs-engine: ncbi-ngs engine was updated - fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
	27	ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries
	28	ngs: Python code will check for the latest version of the libraries and update if newer ones are available
	29	ngs: check for the latest version of the libraries and update if newer ones are available
	30	ngs: simplified ngs-python bindings