[packages/ncbi-blast+] - new , based on fedora
baggins
baggins at pld-linux.org
Thu Feb 20 16:52:44 CET 2014
commit 0ad0a47a85c8a99895644eedb8a8e9944cffc48a
Author: Jan Rękorajski <baggins at pld-linux.org>
Date: Thu Feb 20 16:52:23 2014 +0100
- new , based on fedora
ncbi-blast+-configure.patch | 13 +
ncbi-blast+-libdeps.patch | 704 ++++++++++++++++++++++++++++++++++++++++++++
ncbi-blast+.spec | 121 ++++++++
3 files changed, 838 insertions(+)
---
diff --git a/ncbi-blast+.spec b/ncbi-blast+.spec
new file mode 100644
index 0000000..f5127ea
--- /dev/null
+++ b/ncbi-blast+.spec
@@ -0,0 +1,121 @@
+Summary: NCBI BLAST+ finds regions of similarity between biological sequences
+Name: ncbi-blast+
+Version: 2.2.29
+Release: 1
+License: Public Domain and MIT
+Group: Applications/Science
+Source0: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-%{version}+-src.tar.gz
+# Source0-md5: 1290360b24448dd79840a6800482b597
+Patch0: %{name}-configure.patch
+Patch1: %{name}-libdeps.patch
+URL: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+BuildRequires: boost-devel
+BuildRequires: bzip2-devel
+BuildRequires: curl-devel
+BuildRequires: db-devel
+BuildRequires: expat-devel
+BuildRequires: fcgi-devel
+BuildRequires: freetds-devel
+BuildRequires: freetype-devel
+BuildRequires: ftgl-devel
+BuildRequires: giflib-devel
+BuildRequires: glew-devel
+BuildRequires: gnutls-devel
+BuildRequires: gsoap-devel
+BuildRequires: hdf5-c++-devel
+BuildRequires: libfuse-devel
+BuildRequires: libgcrypt
+#BuildRequires: libgssapi_krb5
+BuildRequires: libicu-devel
+BuildRequires: libjpeg-devel
+BuildRequires: libmagic-devel
+BuildRequires: libpng-devel
+BuildRequires: libtiff-devel
+BuildRequires: libuuid-devel
+BuildRequires: libxml2-devel
+BuildRequires: libxslt-devel
+BuildRequires: libxslt-devel
+BuildRequires: libxslt-progs
+BuildRequires: Mesa-libOSMesa-devel
+BuildRequires: mongodb-devel
+BuildRequires: muparser-devel
+BuildRequires: mysql-devel
+BuildRequires: OpenGL-devel
+BuildRequires: OpenGL-glut-devel
+BuildRequires: openssl-devel
+BuildRequires: pcre-devel
+BuildRequires: perl-devel
+BuildRequires: python-devel
+BuildRequires: sablotron-devel
+BuildRequires: sqlite3-devel
+BuildRequires: wxWidgets-devel
+BuildRequires: xalan-c-devel
+BuildRequires: xerces-c-devel
+BuildRequires: xorg-lib-libICE-devel
+BuildRequires: xorg-lib-libXext-devel
+BuildRequires: xorg-lib-libXmu-devel
+BuildRequires: xorg-lib-libXpm-devel
+BuildRequires: xorg-lib-libXt-devel
+BuildRequires: zlib-devel
+BuildRoot: %{tmpdir}/%{name}-%{version}-root-%(id -u -n)
+
+%description
+The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
+local similarity between sequences. The program compares nucleotide or
+protein sequences to sequence databases and calculates the statistical
+significance of matches. BLAST can be used to infer functional and
+evolutionary relationships between sequences as well as help identify
+members of gene families.
+
+%prep
+%setup -q -n ncbi-blast-%{version}+-src
+%patch0 -p1
+%patch1 -p1
+
+%build
+export CFLAGS="%{rpmcflags}"
+export CXXFLAGS="%{rpmcxxflags}"
+
+cd c++
+%configure \
+ --with-dll \
+ --with-mt \
+ --without-autodep \
+ --without-makefile-auto-update \
+ --with-flat-makefile \
+ --without-caution \
+ --without-dbapi \
+ --without-lzo \
+ --with-runpath=%{_libdir}/ncbi-blast+ \
+ --with-build-root=BUILD \
+ --without-strip \
+ --with-symbols
+
+cd BUILD/build
+%{__make} -f Makefile.flat all_projects="algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/"
+
+%install
+rm -rf $RPM_BUILD_ROOT
+install -d $RPM_BUILD_ROOT/{%{_bindir},%{_libdir}/ncbi-blast+}
+
+install -p c++/BUILD/lib/*.so $RPM_BUILD_ROOT/%{_libdir}/ncbi-blast+
+
+cd c++/BUILD/bin
+install -p blastp blastn blastx tblastn tblastx psiblast rpsblast \
+ rpstblastn blast_formatter deltablast makembindex segmasker \
+ dustmasker windowmasker makeblastdb makeprofiledb blastdbcmd \
+ blastdb_aliastool convert2blastmask blastdbcheck legacy_blast.pl \
+ blastdbcp gene_info_reader seedtop seqdb_demo seqdb_perf datatool \
+ project_tree_builder update_blastdb.pl $RPM_BUILD_ROOT/%{_bindir}
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%files
+%defattr(644,root,root,755)
+%doc c++/scripts/projects/blast/ChangeLog
+%doc c++/scripts/projects/blast/README
+%doc c++/scripts/projects/blast/LICENSE
+%attr(755,root,root) %{_bindir}/*
+%dir %{_libdir}/ncbi-blast+
+%attr(755,root,root) %{_libdir}/ncbi-blast+/*.so
diff --git a/ncbi-blast+-configure.patch b/ncbi-blast+-configure.patch
new file mode 100644
index 0000000..0747338
--- /dev/null
+++ b/ncbi-blast+-configure.patch
@@ -0,0 +1,13 @@
+diff --git a/c++/src/build-system/configure b/c++/src/build-system/configure
+index f58f2e5..6b38355 100755
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -3021,7 +3021,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;}
+ * )
+ { { echo "$as_me:$LINENO: error: $x_arg: unknown option; use --help to show usage" >&5
+ echo "$as_me: error: $x_arg: unknown option; use --help to show usage" >&2;}
+- { (exit 1); exit 1; }; }
++ }
+ ;;
+ esac
+ done
diff --git a/ncbi-blast+-libdeps.patch b/ncbi-blast+-libdeps.patch
new file mode 100644
index 0000000..72b7078
--- /dev/null
+++ b/ncbi-blast+-libdeps.patch
@@ -0,0 +1,704 @@
+diff --git a/c++/src/algo/blast/Makefile.blast_macros.mk b/c++/src/algo/blast/Makefile.blast_macros.mk
+index c135b9b..1976029 100644
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk
+@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
+ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
+
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
++BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
+ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
+ $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+diff --git a/c++/src/algo/blast/api/Makefile.xblast.lib b/c++/src/algo/blast/api/Makefile.xblast.lib
+index 2eca751..6f9c105 100644
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib
+@@ -74,14 +74,15 @@ cdd_pssm_input \
+ deltablast_options \
+ deltablast
+
+-SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
+
+ LIB = xblast
+
+ DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
+ xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
+ blastdb xnetblastcli xnetblast scoremat xconnect tables \
+- $(SOBJMGR_LIBS)
++ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
++ xser xconnect sequtil tables xutil xncbi
+
+ CFLAGS = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+diff --git a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+index d245004..e7c4865 100644
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
+
+ LIB = blastinput
+
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
++DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xutil \
++ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
++scoremat seqset seq xser xutil xncbi
+
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+diff --git a/c++/src/algo/blast/core/Makefile.blast.lib b/c++/src/algo/blast/core/Makefile.blast.lib
+index f37a42b..70f4380 100644
+--- a/c++/src/algo/blast/core/Makefile.blast.lib
++++ b/c++/src/algo/blast/core/Makefile.blast.lib
+@@ -21,5 +21,6 @@ LIB = blast
+ CFLAGS = $(FAST_CFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = composition_adjustment xconnect tables
+
+ WATCHERS = maning madden camacho
+diff --git a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+index fcfb9f9..1a26d31 100644
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
++
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
+diff --git a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+index 41a2509..d5a813c 100644
+--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
++++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+@@ -2,7 +2,7 @@ APP = makembindex
+ SRC = main mkindex_app
+
+ LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
+- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
++ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/algo/blast/format/Makefile.xblastformat.lib b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+index 3058881..dec049f 100644
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,7 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec
+
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
+
+-DLL_LIB = align_format blastxml xhtml xcgi
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
++ seq general xser tables xncbi
+
+ WATCHERS = jianye zaretska madden camacho fongah2
+diff --git a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+index 84e2568..395a551 100644
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -8,6 +8,8 @@ LIB = xalgodustmask
+
+ SRC = symdust
+
++DLL_LIB = xobjmgr seq xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+diff --git a/c++/src/algo/segmask/Makefile.xalgosegmask.lib b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+index bd011c1..713242a 100644
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -8,6 +8,8 @@ LIB = xalgosegmask
+
+ SRC = segmask
+
++DLL_LIB = blast xobjmgr xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+diff --git a/c++/src/algo/winmask/Makefile.xalgowinmask.lib b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+index afaf676..d18c0df 100644
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+diff --git a/c++/src/cgi/Makefile.cgi.lib b/c++/src/cgi/Makefile.cgi.lib
+index fb543d7..31d15b8 100644
+--- a/c++/src/cgi/Makefile.cgi.lib
++++ b/c++/src/cgi/Makefile.cgi.lib
+@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncbires ref_args cgi_run cgi_util \
+ user_agent
+ LIB = xcgi
+
++DLL_LIB = xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+
+ WATCHERS = vakatov
+diff --git a/c++/src/connect/Makefile.xconnect.lib b/c++/src/connect/Makefile.xconnect.lib
+index 473bb0b..08c7014 100644
+--- a/c++/src/connect/Makefile.xconnect.lib
++++ b/c++/src/connect/Makefile.xconnect.lib
+@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
+ LIB = xconnect
+ PROJ_TAG = core
+
++DLL_LIB = xncbi
++
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+
+ WATCHERS = lavr
+diff --git a/c++/src/connect/ext/Makefile.xconnext.lib b/c++/src/connect/ext/Makefile.xconnext.lib
+index 3c4875d..8cc5a9f 100644
+--- a/c++/src/connect/ext/Makefile.xconnext.lib
++++ b/c++/src/connect/ext/Makefile.xconnext.lib
+@@ -6,4 +6,6 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper
+
+ LIB = xconnext
+
++DLL_LIB = xconnect xncbi
++
+ WATCHERS = lavr
+diff --git a/c++/src/corelib/Makefile.test_boost.lib b/c++/src/corelib/Makefile.test_boost.lib
+index 9d34c45..f978a60 100644
+--- a/c++/src/corelib/Makefile.test_boost.lib
++++ b/c++/src/corelib/Makefile.test_boost.lib
+@@ -3,6 +3,8 @@
+ SRC = test_boost
+ LIB = test_boost
+
++DLL_LIB = xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
+
+ REQUIRES = Boost.Test.Included
+diff --git a/c++/src/corelib/Makefile.test_mt.lib b/c++/src/corelib/Makefile.test_mt.lib
+index 6153eab..2f1d737 100644
+--- a/c++/src/corelib/Makefile.test_mt.lib
++++ b/c++/src/corelib/Makefile.test_mt.lib
+@@ -3,6 +3,8 @@
+ SRC = test_mt
+ LIB = test_mt
+
++DLL_LIB = xncbi
++
+ # REQUIRES = MT
+
+ USE_PCH = no
+diff --git a/c++/src/html/Makefile.html.lib b/c++/src/html/Makefile.html.lib
+index 6d08b9e..e7377bd 100644
+--- a/c++/src/html/Makefile.html.lib
++++ b/c++/src/html/Makefile.html.lib
+@@ -7,4 +7,6 @@ SRC = node html htmlhelper page pager selection components \
+ commentdiag indentstream html_exception writer_htmlenc
+ LIB = xhtml
+
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+diff --git a/c++/src/objects/biblio/Makefile.biblio.lib b/c++/src/objects/biblio/Makefile.biblio.lib
+index 2c7d491..31125ad 100644
+--- a/c++/src/objects/biblio/Makefile.biblio.lib
++++ b/c++/src/objects/biblio/Makefile.biblio.lib
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ citation_base
++
++DLL_LIB = general xser xncbi
+diff --git a/c++/src/objects/blast/Makefile.blast.lib b/c++/src/objects/blast/Makefile.blast.lib
+index 0dd0fa3..9d68feb 100644
+--- a/c++/src/objects/blast/Makefile.blast.lib
++++ b/c++/src/objects/blast/Makefile.blast.lib
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+diff --git a/c++/src/objects/blast/Makefile.xnetblastcli.lib b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+index 96325c4..6bd755e 100644
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+@@ -2,3 +2,5 @@ ASN_DEP = xnetblast
+
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+diff --git a/c++/src/objects/blastdb/Makefile.blastdb.lib b/c++/src/objects/blastdb/Makefile.blastdb.lib
+index 5f0ecc7..a028153 100644
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
+@@ -1,5 +1,7 @@
+ # $Id: Makefile.blastdb.lib 395653 2013-04-12 14:33:22Z vakatov $
+
++
++DLL_LIB = seq xser xncbi
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
+
+diff --git a/c++/src/objects/blastxml/Makefile.blastxml.lib b/c++/src/objects/blastxml/Makefile.blastxml.lib
+index d18eb78..0e98c29 100644
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
++
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/entrez2/Makefile.entrez2.lib b/c++/src/objects/entrez2/Makefile.entrez2.lib
+index 4507f72..0bff536 100644
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
+@@ -2,3 +2,5 @@ WATCHERS = lavr
+
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/entrez2/Makefile.entrez2cli.lib b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+index 42a4649..dc01ad5 100644
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -4,3 +4,5 @@ ASN_DEP = entrez2
+
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+diff --git a/c++/src/objects/general/Makefile.general.lib b/c++/src/objects/general/Makefile.general.lib
+index 951304f..417d1ed 100644
+--- a/c++/src/objects/general/Makefile.general.lib
++++ b/c++/src/objects/general/Makefile.general.lib
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/genomecoll/Makefile.genome_collection.lib b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+index f039af6..9f733a0 100644
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+@@ -3,4 +3,6 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio
+diff --git a/c++/src/objects/id1/Makefile.id1.lib b/c++/src/objects/id1/Makefile.id1.lib
+index d60c728..3ac9022 100644
+--- a/c++/src/objects/id1/Makefile.id1.lib
++++ b/c++/src/objects/id1/Makefile.id1.lib
+@@ -3,4 +3,6 @@ ASN_DEP = seq
+ LIB = id1
+ SRC = id1__ id1___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objects/id2/Makefile.id2.lib b/c++/src/objects/id2/Makefile.id2.lib
+index 09d8b36..ea8b07f 100644
+--- a/c++/src/objects/id2/Makefile.id2.lib
++++ b/c++/src/objects/id2/Makefile.id2.lib
+@@ -1,4 +1,6 @@
+ LIB = id2
+ SRC = id2__ id2___
+
++DLL_LIB = seqsplit seq xser xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objects/medline/Makefile.medline.lib b/c++/src/objects/medline/Makefile.medline.lib
+index ea28066..0b9b02a 100644
+--- a/c++/src/objects/medline/Makefile.medline.lib
++++ b/c++/src/objects/medline/Makefile.medline.lib
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = biblio general xser xncbi
+diff --git a/c++/src/objects/pub/Makefile.pub.lib b/c++/src/objects/pub/Makefile.pub.lib
+index 78c12e1..d873e1c 100644
+--- a/c++/src/objects/pub/Makefile.pub.lib
++++ b/c++/src/objects/pub/Makefile.pub.lib
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio xser xncbi
+diff --git a/c++/src/objects/scoremat/Makefile.scoremat.lib b/c++/src/objects/scoremat/Makefile.scoremat.lib
+index 62e01f5..7664a1b 100644
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+diff --git a/c++/src/objects/seq/Makefile.seq.lib b/c++/src/objects/seq/Makefile.seq.lib
+index 1b5edc5..dcc8b58 100644
+--- a/c++/src/objects/seq/Makefile.seq.lib
++++ b/c++/src/objects/seq/Makefile.seq.lib
+@@ -12,4 +12,6 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
+ seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
+ seq_loc_from_string seq_loc_reverse_complementer
+
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = vasilche grichenk
+diff --git a/c++/src/objects/seqcode/Makefile.seqcode.lib b/c++/src/objects/seqcode/Makefile.seqcode.lib
+index dc9d60e..9a7e296 100644
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/seqedit/Makefile.seqedit.lib b/c++/src/objects/seqedit/Makefile.seqedit.lib
+index 283a9b7..fdc7574 100644
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+-
++
++DLL_LIB = seqset seq general xser xncbi
+diff --git a/c++/src/objects/seqset/Makefile.seqset.lib b/c++/src/objects/seqset/Makefile.seqset.lib
+index 87f16d0..bcd250d 100644
+--- a/c++/src/objects/seqset/Makefile.seqset.lib
++++ b/c++/src/objects/seqset/Makefile.seqset.lib
+@@ -1,2 +1,4 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++
++DLL_LIB = seq general xser xncbi
+diff --git a/c++/src/objects/seqsplit/Makefile.seqsplit.lib b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+index 87ae869..7ac4405 100644
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+@@ -1,4 +1,6 @@
+ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objects/submit/Makefile.submit.lib b/c++/src/objects/submit/Makefile.submit.lib
+index 74798f8..b034f64 100644
+--- a/c++/src/objects/submit/Makefile.submit.lib
++++ b/c++/src/objects/submit/Makefile.submit.lib
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+diff --git a/c++/src/objmgr/split/Makefile.id2_split.lib b/c++/src/objmgr/split/Makefile.id2_split.lib
+index fafa70a..4ef60c7 100644
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib
+@@ -17,6 +17,6 @@ LIB = id2_split
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+
+ WATCHERS = vasilche
+diff --git a/c++/src/objmgr/util/Makefile.util.lib b/c++/src/objmgr/util/Makefile.util.lib
+index 4001243..bacc47c 100644
+--- a/c++/src/objmgr/util/Makefile.util.lib
++++ b/c++/src/objmgr/util/Makefile.util.lib
+@@ -7,6 +7,7 @@ ASN_DEP = submit
+
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
+ LIB = xobjutil
++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
+
+ WATCHERS = ucko vasilche kornbluh
+
+diff --git a/c++/src/objtools/align_format/Makefile.align_format.lib b/c++/src/objtools/align_format/Makefile.align_format.lib
+index 1ec5bf0..b0d70c7 100644
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib
+@@ -13,6 +13,10 @@ SRC = format_flags align_format_util showdefline showalign tabular vectorscreen
+
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
+
++DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
++ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
++ xcgi xhtml tables xncbi
++
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CFLAGS = $(FAST_CFLAGS)
+ # CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+index e32c351..3f44394 100644
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+@@ -12,3 +12,5 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \
+
+ WATCHERS = todorov dicuccio grichenk
+
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
++
+diff --git a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+index 62f01fd..b877f98 100644
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
++++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract blastdb_formatter
+
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+
++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
+
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CFLAGS = $(FAST_CFLAGS)
+diff --git a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+index 3a92e3e..79a75b9 100644
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
++++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+@@ -5,3 +5,5 @@ WATCHERS = camacho
+ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG_CPPFLAGS)
+ LIB = gene_info
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+diff --git a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+index 9c13307..ed8c4ae 100644
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+@@ -24,6 +24,8 @@ seqdbobj
+
+ LIB = seqdb
+
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+index 8929b72..31b9ce7 100644
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volume writedb_files writedb_isam writedb_gim
+
+ LIB = writedb
+
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
++ xser sequtil xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/blast/services/Makefile.blast_services.lib b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+index ceba356..cd3b1ba 100644
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+@@ -8,6 +8,8 @@ SRC = blast_services
+
+ LIB = blast_services
+
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+index 4fb6117..837108e 100644
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+@@ -7,4 +7,6 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+
+ ASN_DEP = blastdb seqset
+
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+index 243467f..e20368e 100644
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapter
+
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
++
+ ASN_DEP = blastdb xnetblast
+
+ WATCHERS = camacho
+diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+index 9ae861b..7a3a9c1 100644
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+@@ -12,4 +12,7 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++ xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+index f3bb947..eccf6d1 100644
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -15,4 +15,7 @@ LIB_OR_DLL = both
+ DLL_LIB =
+ DLL_DLIB = $(GENBANK_READER_LDEP)
+
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++ xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+index f3164f5..98a627c 100644
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+index c6f8076..0bcc0c5 100644
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+index 0a29cbf..c5c4b6a 100644
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
++++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+@@ -12,6 +12,9 @@ LIB_OR_DLL = both
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
+
+ # Dependencies for shared library (disabled due to problems on Darwin)
+-# DLL_LIB = xconnect ncbi_xreader$(DLL)
++DLL_LIB = xconnect ncbi_xreader$(DLL)
++
++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
++
+
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/readers/Makefile.xobjread.lib b/c++/src/objtools/readers/Makefile.xobjread.lib
+index eae8a72..15f2cec 100644
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib
+@@ -20,5 +20,5 @@ SRC = read_util format_guess_ex \
+ message_listener line_error
+
+
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi submit
+
+diff --git a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+index 8115a7f..88bfd38 100644
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -12,6 +12,6 @@ mask_writer_seqloc \
+ mask_writer_blastdb_maskinfo
+
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
+
+ WATCHERS = morgulis camacho
+diff --git a/c++/src/objtools/simple/Makefile.xobjsimple.lib b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+index dab25d6..1dc389d 100644
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+@@ -7,6 +7,8 @@ WATCHERS = jcherry
+
+ ASN_DEP = seqset
+
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
++
+ LIB = xobjsimple
+ SRC = simple_om
+
+diff --git a/c++/src/serial/Makefile.serial.lib b/c++/src/serial/Makefile.serial.lib
+index 2563b5f..116ad11 100644
+--- a/c++/src/serial/Makefile.serial.lib
++++ b/c++/src/serial/Makefile.serial.lib
+@@ -18,4 +18,6 @@ SRC = \
+
+ LIB = xser
+
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+diff --git a/c++/src/util/Makefile.util.lib b/c++/src/util/Makefile.util.lib
+index 25654a5..3613b12 100644
+--- a/c++/src/util/Makefile.util.lib
++++ b/c++/src/util/Makefile.util.lib
+@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \
+ LIB = xutil
+ PROJ_TAG = core
+
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+
+ WATCHERS = vakatov kornbluh
+diff --git a/c++/src/util/compress/api/Makefile.compress.lib b/c++/src/util/compress/api/Makefile.compress.lib
+index 5e5d3d6..baeab24 100644
+--- a/c++/src/util/compress/api/Makefile.compress.lib
++++ b/c++/src/util/compress/api/Makefile.compress.lib
+@@ -7,7 +7,7 @@ LIB = xcompress
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
+ LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
+
+ WATCHERS = ivanov
+diff --git a/c++/src/util/sequtil/Makefile.sequtil.lib b/c++/src/util/sequtil/Makefile.sequtil.lib
+index c068a32..003d3d3 100644
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib
+@@ -3,4 +3,6 @@
+ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+diff --git a/c++/src/util/xregexp/Makefile.xregexp.lib b/c++/src/util/xregexp/Makefile.xregexp.lib
+index 965fac4..508a058 100644
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
+@@ -6,7 +6,7 @@ LIB = xregexp
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS = $(PCRE_LIBS)
+
+ WATCHERS = ivanov
================================================================
---- gitweb:
http://git.pld-linux.org/gitweb.cgi/packages/ncbi-blast+.git/commitdiff/0ad0a47a85c8a99895644eedb8a8e9944cffc48a
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