First working patch

Signed-off-by: Justin Lecher <jlec@gentoo.org>

1 files changed, 602 insertions, 156 deletions

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index 610ee24ab..f5d6a3d67 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
@@ -1,135 +1,184 @@
- src/algo/align/ngalign/Makefile.xngalign.lib                        | 2 ++
- src/algo/blast/api/Makefile.xblast.lib                              | 2 +-
- src/algo/blast/blastinput/Makefile.blastinput.lib                   | 2 +-
- src/algo/blast/core/Makefile.blast.lib                              | 2 ++
- src/algo/cobalt/Makefile.cobalt.lib                                 | 2 ++
- src/algo/ms/omssa/Makefile.xomssa.lib                               | 2 ++
- src/algo/sequence/Makefile.xalgoseq.lib                             | 2 ++
- src/algo/structure/struct_dp/Makefile.xstruct_dp.lib                | 2 ++
- src/algo/structure/struct_util/Makefile.xstruct_util.lib            | 2 ++
- src/algo/structure/threader/Makefile.xstruct_thread.lib             | 2 ++
- src/algo/winmask/Makefile.xalgowinmask.lib                          | 1 +
- src/cgi/Makefile.cgi.lib                                            | 2 ++
- src/cgi/Makefile.fcgi.lib                                           | 2 ++
- src/connect/Makefile.connssl.lib                                    | 2 ++
- src/connect/Makefile.xconnect.lib                                   | 4 ++++
- src/connect/Makefile.xthrserv.lib                                   | 2 +-
- src/connect/Makefile.xxconnect.lib                                  | 2 ++
- src/connect/services/Makefile.ncbi_xcache_netcache.lib              | 2 +-
- src/connect/services/Makefile.xconnserv.lib                         | 2 +-
- src/connect/test/Makefile.conntest.lib                              | 2 ++
- src/corelib/Makefile.test_boost.lib                                 | 2 ++
- src/corelib/Makefile.test_mt.lib                                    | 2 ++
- src/corelib/test/Makefile.pbacktest.lib                             | 2 ++
- src/db/bdb/Makefile.bdb.lib                                         | 4 ++++
- src/db/bdb/Makefile.ncbi_xcache_bdb.lib                             | 2 +-
- src/db/sqlite/Makefile.sqlitewrapp.lib                              | 3 +++
- src/dbapi/Makefile.dbapi.lib                                        | 5 +++++
- src/dbapi/driver/Makefile.dbapi_driver.lib                          | 2 ++
- src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib             | 2 ++
- src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib           | 2 +-
- src/dbapi/simple/Makefile.sdbapi.lib                                | 1 +
- src/html/Makefile.html.lib                                          | 2 ++
- src/objects/access/Makefile.access.lib                              | 1 +
- src/objects/biblio/Makefile.biblio.lib                              | 2 ++
- src/objects/biotree/Makefile.biotree.lib                            | 2 ++
- src/objects/blast/Makefile.blast.lib                                | 2 ++
- src/objects/blast/Makefile.xnetblastcli.lib                         | 2 ++
- src/objects/blastdb/Makefile.blastdb.lib                            | 2 ++
- src/objects/blastxml/Makefile.blastxml.lib                          | 2 ++
- src/objects/cdd/Makefile.cdd.lib                                    | 2 ++
- src/objects/cn3d/Makefile.cn3d.lib                                  | 2 ++
- src/objects/docsum/Makefile.docsum.lib                              | 2 ++
- src/objects/entrez2/Makefile.entrez2.lib                            | 2 ++
- src/objects/entrez2/Makefile.entrez2cli.lib                         | 2 ++
- src/objects/entrezgene/Makefile.entrezgene.lib                      | 2 ++
- src/objects/featdef/Makefile.featdef.lib                            | 2 ++
- src/objects/gbseq/Makefile.gbseq.lib                                | 2 ++
- src/objects/general/Makefile.general.lib                            | 2 ++
- src/objects/genomecoll/Makefile.genome_collection.lib               | 2 ++
- src/objects/homologene/Makefile.homologene.lib                      | 2 ++
- src/objects/id1/Makefile.id1.lib                                    | 2 ++
- src/objects/id1/Makefile.id1cli.lib                                 | 2 ++
- src/objects/id2/Makefile.id2.lib                                    | 2 ++
- src/objects/id2/Makefile.id2cli.lib                                 | 2 ++
- src/objects/insdseq/Makefile.insdseq.lib                            | 2 ++
- src/objects/macro/Makefile.macro.lib                                | 2 ++
- src/objects/medlars/Makefile.medlars.lib                            | 2 ++
- src/objects/medline/Makefile.medline.lib                            | 2 ++
- src/objects/mim/Makefile.mim.lib                                    | 2 ++
- src/objects/mla/Makefile.mla.lib                                    | 2 ++
- src/objects/mla/Makefile.mlacli.lib                                 | 2 ++
- src/objects/mmdb/Makefile.mmdb.lib                                  | 2 ++
- src/objects/ncbimime/Makefile.ncbimime.lib                          | 2 ++
- src/objects/objprt/Makefile.objprt.lib                              | 2 ++
- src/objects/omssa/Makefile.omssa.lib                                | 2 ++
- src/objects/pcassay/Makefile.pcassay.lib                            | 2 ++
- src/objects/pcsubstance/Makefile.pcsubstance.lib                    | 2 ++
- src/objects/proj/Makefile.proj.lib                                  | 2 ++
- src/objects/pub/Makefile.pub.lib                                    | 2 ++
- src/objects/pubmed/Makefile.pubmed.lib                              | 2 ++
- src/objects/remap/Makefile.remap.lib                                | 2 ++
- src/objects/remap/Makefile.remapcli.lib                             | 2 ++
- src/objects/scoremat/Makefile.scoremat.lib                          | 2 ++
- src/objects/seq/Makefile.seq.lib                                    | 2 ++
- src/objects/seqcode/Makefile.seqcode.lib                            | 2 ++
- src/objects/seqedit/Makefile.seqedit.lib                            | 1 +
- src/objects/seqset/Makefile.seqset.lib                              | 1 +
- src/objects/seqsplit/Makefile.seqsplit.lib                          | 2 ++
- src/objects/seqtest/Makefile.seqtest.lib                            | 2 ++
- src/objects/submit/Makefile.submit.lib                              | 1 +
- src/objects/taxon1/Makefile.taxon1.lib                              | 2 ++
- src/objects/taxon3/Makefile.taxon3.lib                              | 2 ++
- src/objects/tinyseq/Makefile.tinyseq.lib                            | 2 ++
- src/objects/valerr/Makefile.valerr.lib                              | 2 ++
- src/objects/valid/Makefile.valid.lib                                | 2 ++
- src/objects/variation/Makefile.variation.lib                        | 1 +
- src/objmgr/split/Makefile.id2_split.lib                             | 2 +-
- src/objmgr/util/Makefile.util.lib                                   | 1 +
- src/objtools/align_format/Makefile.align_format.lib                 | 2 ++
- src/objtools/alnmgr/Makefile.alnmgr.lib                             | 1 +
- src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib       | 2 ++
- src/objtools/blast/gene_info_reader/Makefile.gene_info.lib          | 2 ++
- src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib   | 2 ++
- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib                  | 2 ++
- src/objtools/blast/seqdb_writer/Makefile.writedb.lib                | 2 ++
- src/objtools/blast/services/Makefile.blast_services.lib             | 1 +
- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++
- src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib         | 2 +-
- src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++
- src/objtools/edit/Makefile.edit.lib                                 | 2 ++
- src/objtools/eutils/egquery/Makefile.egquery.lib                    | 2 ++
- src/objtools/eutils/ehistory/Makefile.ehistory.lib                  | 2 ++
- src/objtools/eutils/einfo/Makefile.einfo.lib                        | 2 ++
- src/objtools/eutils/elink/Makefile.elink.lib                        | 2 ++
- src/objtools/eutils/epost/Makefile.epost.lib                        | 2 ++
- src/objtools/eutils/esearch/Makefile.esearch.lib                    | 2 ++
- src/objtools/eutils/espell/Makefile.espell.lib                      | 2 ++
- src/objtools/eutils/esummary/Makefile.esummary.lib                  | 2 ++
- src/objtools/eutils/linkout/Makefile.linkout.lib                    | 2 ++
- src/objtools/format/Makefile.xformat.lib                            | 2 ++
- src/objtools/lds/Makefile.lds.lib                                   | 2 +-
- src/objtools/manip/Makefile.xobjmanip.lib                           | 2 ++
- src/objtools/readers/Makefile.xobjread.lib                          | 3 +--
- src/objtools/readers/Makefile.xobjreadex.lib                        | 2 +-
- src/objtools/simple/Makefile.xobjsimple.lib                         | 1 +
- src/objtools/validator/Makefile.validator.lib                       | 2 ++
- src/objtools/writers/Makefile.xobjwrite.lib                         | 1 +
- src/serial/Makefile.serial.lib                                      | 2 ++
- src/serial/soap/Makefile.soap.lib                                   | 2 ++
- src/serial/soap/Makefile.soap_server.lib                            | 2 ++
- src/serial/test/Makefile.we_cpp.lib                                 | 1 +
- src/sra/sdk/libs/align/Makefile.align-writer.lib                    | 2 +-
- src/util/Makefile.util.lib                                          | 2 ++
- src/util/compress/api/Makefile.compress.lib                         | 2 +-
- src/util/qparse/Makefile.xqueryparse.lib                            | 2 ++
- src/util/regexp/Makefile.regexp.lib                                 | 2 ++
- src/util/sequtil/Makefile.sequtil.lib                               | 2 ++
- src/util/xregexp/Makefile.xregexp.lib                               | 2 +-
- 128 files changed, 237 insertions(+), 16 deletions(-)
+ src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib     | 2 ++
+ src/algo/align/ngalign/Makefile.xngalign.lib                         | 2 ++
+ src/algo/align/nw/Makefile.xalgoalignnw.lib                          | 2 ++
+ src/algo/align/prosplign/Makefile.prosplign.lib                      | 2 ++
+ src/algo/align/splign/Makefile.xalgoalignsplign.lib                  | 2 ++
+ src/algo/blast/api/Makefile.xblast.lib                               | 2 +-
+ src/algo/blast/blastinput/Makefile.blastinput.lib                    | 2 +-
+ src/algo/blast/core/Makefile.blast.lib                               | 2 ++
+ src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib                | 2 ++
+ src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib  | 2 ++
+ src/algo/blast/format/Makefile.xblastformat.lib                      | 2 +-
+ src/algo/blast/gumbel_params/Makefile.gumbelparams.lib               | 1 +
+ src/algo/cobalt/Makefile.cobalt.lib                                  | 2 ++
+ src/algo/dustmask/Makefile.xalgodustmask.lib                         | 1 +
+ src/algo/gnomon/Makefile.gnomon.lib                                  | 2 +-
+ src/algo/ms/formats/pepxml/Makefile.pepXML.lib                       | 2 ++
+ src/algo/ms/omssa/Makefile.xomssa.lib                                | 2 ++
+ src/algo/phy_tree/Makefile.xalgophytree.lib                          | 2 +-
+ src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib          | 2 ++
+ src/algo/segmask/Makefile.xalgosegmask.lib                           | 1 +
+ src/algo/seqqa/Makefile.xalgoseqqa.lib                               | 2 ++
+ src/algo/sequence/Makefile.xalgoseq.lib                              | 2 ++
+ src/algo/structure/bma_refine/Makefile.xbma_refiner.lib              | 3 +++
+ src/algo/structure/cd_utils/Makefile.xcd_utils.lib                   | 2 +-
+ src/algo/structure/struct_dp/Makefile.xstruct_dp.lib                 | 2 ++
+ src/algo/structure/struct_util/Makefile.xstruct_util.lib             | 2 ++
+ src/algo/structure/threader/Makefile.xstruct_thread.lib              | 2 ++
+ src/algo/text/Makefile.xalgotext.lib                                 | 2 ++
+ src/algo/volume_merge/Makefile.xalgovmerge.lib                       | 2 ++
+ src/algo/winmask/Makefile.xalgowinmask.lib                           | 2 ++
+ src/cgi/Makefile.cgi.lib                                             | 2 ++
+ src/cgi/Makefile.fcgi.lib                                            | 2 ++
+ src/connect/Makefile.connssl.lib                                     | 2 ++
+ src/connect/Makefile.xconnect.lib                                    | 4 ++++
+ src/connect/Makefile.xthrserv.lib                                    | 2 +-
+ src/connect/Makefile.xxconnect.lib                                   | 2 ++
+ src/connect/services/Makefile.ncbi_xcache_netcache.lib               | 2 +-
+ src/connect/services/Makefile.xconnserv.lib                          | 2 +-
+ src/connect/test/Makefile.conntest.lib                               | 2 ++
+ src/corelib/Makefile.test_boost.lib                                  | 2 ++
+ src/corelib/Makefile.test_mt.lib                                     | 2 ++
+ src/corelib/test/Makefile.pbacktest.lib                              | 2 ++
+ src/db/bdb/Makefile.bdb.lib                                          | 4 ++++
+ src/db/bdb/Makefile.ncbi_xcache_bdb.lib                              | 2 +-
+ src/db/sqlite/Makefile.sqlitewrapp.lib                               | 3 +++
+ src/dbapi/Makefile.dbapi.lib                                         | 5 +++++
+ src/dbapi/driver/Makefile.dbapi_driver.lib                           | 2 ++
+ src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib              | 2 ++
+ src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib            | 2 +-
+ src/dbapi/simple/Makefile.sdbapi.lib                                 | 1 +
+ src/html/Makefile.html.lib                                           | 2 ++
+ src/misc/cgi_redirect/Makefile.cgi_redirect.lib                      | 2 ++
+ src/misc/grid_cgi/Makefile.xgridcgi.lib                              | 2 ++
+ src/objects/access/Makefile.access.lib                               | 1 +
+ src/objects/biblio/Makefile.biblio.lib                               | 2 ++
+ src/objects/biotree/Makefile.biotree.lib                             | 2 ++
+ src/objects/blast/Makefile.blast.lib                                 | 2 ++
+ src/objects/blast/Makefile.xnetblastcli.lib                          | 2 ++
+ src/objects/blastdb/Makefile.blastdb.lib                             | 2 ++
+ src/objects/blastxml/Makefile.blastxml.lib                           | 2 ++
+ src/objects/cdd/Makefile.cdd.lib                                     | 2 ++
+ src/objects/cn3d/Makefile.cn3d.lib                                   | 2 ++
+ src/objects/docsum/Makefile.docsum.lib                               | 2 ++
+ src/objects/entrez2/Makefile.entrez2.lib                             | 2 ++
+ src/objects/entrez2/Makefile.entrez2cli.lib                          | 2 ++
+ src/objects/entrezgene/Makefile.entrezgene.lib                       | 2 ++
+ src/objects/featdef/Makefile.featdef.lib                             | 2 ++
+ src/objects/gbseq/Makefile.gbseq.lib                                 | 2 ++
+ src/objects/general/Makefile.general.lib                             | 2 ++
+ src/objects/genomecoll/Makefile.genome_collection.lib                | 2 ++
+ src/objects/homologene/Makefile.homologene.lib                       | 2 ++
+ src/objects/id1/Makefile.id1.lib                                     | 2 ++
+ src/objects/id1/Makefile.id1cli.lib                                  | 2 ++
+ src/objects/id2/Makefile.id2.lib                                     | 2 ++
+ src/objects/id2/Makefile.id2cli.lib                                  | 2 ++
+ src/objects/insdseq/Makefile.insdseq.lib                             | 2 ++
+ src/objects/macro/Makefile.macro.lib                                 | 2 ++
+ src/objects/medlars/Makefile.medlars.lib                             | 2 ++
+ src/objects/medline/Makefile.medline.lib                             | 2 ++
+ src/objects/mim/Makefile.mim.lib                                     | 2 ++
+ src/objects/mla/Makefile.mla.lib                                     | 2 ++
+ src/objects/mla/Makefile.mlacli.lib                                  | 2 ++
+ src/objects/mmdb/Makefile.mmdb.lib                                   | 2 ++
+ src/objects/ncbimime/Makefile.ncbimime.lib                           | 2 ++
+ src/objects/objprt/Makefile.objprt.lib                               | 2 ++
+ src/objects/omssa/Makefile.omssa.lib                                 | 2 ++
+ src/objects/pcassay/Makefile.pcassay.lib                             | 2 ++
+ src/objects/pcsubstance/Makefile.pcsubstance.lib                     | 2 ++
+ src/objects/proj/Makefile.proj.lib                                   | 2 ++
+ src/objects/pub/Makefile.pub.lib                                     | 2 ++
+ src/objects/pubmed/Makefile.pubmed.lib                               | 2 ++
+ src/objects/remap/Makefile.remap.lib                                 | 2 ++
+ src/objects/remap/Makefile.remapcli.lib                              | 2 ++
+ src/objects/scoremat/Makefile.scoremat.lib                           | 2 ++
+ src/objects/seq/Makefile.seq.lib                                     | 2 ++
+ src/objects/seqcode/Makefile.seqcode.lib                             | 2 ++
+ src/objects/seqedit/Makefile.seqedit.lib                             | 1 +
+ src/objects/seqset/Makefile.seqset.lib                               | 1 +
+ src/objects/seqsplit/Makefile.seqsplit.lib                           | 2 ++
+ src/objects/seqtest/Makefile.seqtest.lib                             | 2 ++
+ src/objects/submit/Makefile.submit.lib                               | 1 +
+ src/objects/taxon1/Makefile.taxon1.lib                               | 2 ++
+ src/objects/taxon3/Makefile.taxon3.lib                               | 2 ++
+ src/objects/tinyseq/Makefile.tinyseq.lib                             | 2 ++
+ src/objects/valerr/Makefile.valerr.lib                               | 2 ++
+ src/objects/valid/Makefile.valid.lib                                 | 2 ++
+ src/objects/variation/Makefile.variation.lib                         | 1 +
+ src/objmgr/split/Makefile.id2_split.lib                              | 2 +-
+ src/objmgr/util/Makefile.util.lib                                    | 1 +
+ src/objtools/align/Makefile.xalntool.lib                             | 2 ++
+ src/objtools/align_format/Makefile.align_format.lib                  | 2 ++
+ src/objtools/alnmgr/Makefile.alnmgr.lib                              | 1 +
+ src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib        | 2 ++
+ src/objtools/blast/gene_info_reader/Makefile.gene_info.lib           | 2 ++
+ src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib    | 2 ++
+ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib                   | 2 ++
+ src/objtools/blast/seqdb_writer/Makefile.writedb.lib                 | 2 ++
+ src/objtools/blast/services/Makefile.blast_services.lib              | 1 +
+ src/objtools/cddalignview/Makefile.cddalignview.lib                  | 2 ++
+ src/objtools/cleanup/Makefile.cleanup.lib                            | 2 +-
+ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib  | 3 +++
+ .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib       | 2 ++
+ src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib          | 2 ++
+ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib          | 2 +-
+ src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib  | 2 ++
+ src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib  | 2 ++
+ src/objtools/data_loaders/trace/Makefile.xloader_trace.lib           | 2 ++
+ src/objtools/edit/Makefile.edit.lib                                  | 2 ++
+ src/objtools/eutils/api/Makefile.eutils.lib                          | 2 ++
+ src/objtools/eutils/egquery/Makefile.egquery.lib                     | 2 ++
+ src/objtools/eutils/ehistory/Makefile.ehistory.lib                   | 2 ++
+ src/objtools/eutils/einfo/Makefile.einfo.lib                         | 2 ++
+ src/objtools/eutils/elink/Makefile.elink.lib                         | 2 ++
+ src/objtools/eutils/epost/Makefile.epost.lib                         | 2 ++
+ src/objtools/eutils/esearch/Makefile.esearch.lib                     | 2 ++
+ src/objtools/eutils/espell/Makefile.espell.lib                       | 2 ++
+ src/objtools/eutils/esummary/Makefile.esummary.lib                   | 2 ++
+ src/objtools/eutils/linkout/Makefile.linkout.lib                     | 2 ++
+ src/objtools/eutils/uilist/Makefile.uilist.lib                       | 2 ++
+ src/objtools/format/Makefile.xformat.lib                             | 2 ++
+ src/objtools/lds/Makefile.lds.lib                                    | 2 +-
+ src/objtools/manip/Makefile.xobjmanip.lib                            | 2 ++
+ src/objtools/readers/Makefile.xobjread.lib                           | 3 +--
+ src/objtools/readers/Makefile.xobjreadex.lib                         | 2 +-
+ src/objtools/seqmasks_io/Makefile.seqmasks_io.lib                    | 2 +-
+ src/objtools/simple/Makefile.xobjsimple.lib                          | 1 +
+ src/objtools/snputil/Makefile.snputil.lib                            | 2 ++
+ src/objtools/validator/Makefile.validator.lib                        | 2 ++
+ src/objtools/writers/Makefile.xobjwrite.lib                          | 1 +
+ src/sample/app/asn/Makefile.sample_asn.lib                           | 2 ++
+ src/sample/app/soap/Makefile.soap_dataobj.lib                        | 2 ++
+ src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib                   | 2 ++
+ src/sample/lib/basic/Makefile.basic_sample_lib.lib                   | 2 ++
+ src/sample/lib/dtd/Makefile.dtd_sample_lib.lib                       | 2 ++
+ src/sample/lib/xsd/Makefile.xsd_sample_lib.lib                       | 2 ++
+ src/serial/Makefile.serial.lib                                       | 2 ++
+ src/serial/soap/Makefile.soap.lib                                    | 2 ++
+ src/serial/soap/Makefile.soap_server.lib                             | 2 ++
+ src/serial/test/Makefile.we_cpp.lib                                  | 1 +
+ src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib               | 2 +-
+ src/sra/sdk/libs/align/Makefile.align-writer.lib                     | 2 +-
+ src/util/Makefile.util.lib                                           | 2 ++
+ src/util/compress/api/Makefile.compress.lib                          | 2 +-
+ src/util/qparse/Makefile.xqueryparse.lib                             | 2 ++
+ src/util/regexp/Makefile.regexp.lib                                  | 2 ++
+ src/util/sequtil/Makefile.sequtil.lib                                | 2 ++
+ src/util/xregexp/Makefile.xregexp.lib                                | 2 +-
+ 167 files changed, 307 insertions(+), 23 deletions(-)
 
+diff --git a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+index c8851d8..35ae629 100644
+--- a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
++++ b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+@@ -10,3 +10,5 @@ LIB = xalgocontig_assembly
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver seq xalgoalignnw xalgodustmask xalnmgr xblast xncbi xobjmgr xobjutil xser # axf
 diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib
-index d163f7c..f9c79ba 100644
+index d163f7c..ade88ce 100644
 --- a/src/algo/align/ngalign/Makefile.xngalign.lib
 +++ b/src/algo/align/ngalign/Makefile.xngalign.lib
 @@ -15,3 +15,5 @@ LIB = xngalign
@@ -137,9 +186,39 @@ index d163f7c..f9c79ba 100644
  CXXFLAGS = $(FAST_CXXFLAGS) -I./. 
  LDFLAGS  = $(FAST_LDFLAGS)
 +
-+DLL_LIB = seq xalgoalignutil xncbi blastinput
++DLL_LIB = seq xalgoalignutil xncbi blastinput xalgoalignnw align_format xcgi  ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2
+diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+index acc1ddf..acba81c 100644
+--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib
++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+@@ -15,3 +15,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+ WATCHERS = kiryutin
++
++DLL_LIB = access align_format dbapi_driver general seq writedb xncbi xser # axf
+diff --git a/src/algo/align/prosplign/Makefile.prosplign.lib b/src/algo/align/prosplign/Makefile.prosplign.lib
+index 248ee37..73143ad 100644
+--- a/src/algo/align/prosplign/Makefile.prosplign.lib
++++ b/src/algo/align/prosplign/Makefile.prosplign.lib
+@@ -10,3 +10,5 @@ LIB = prosplign
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver general igblast seq xalgoalignutil xalnmgr xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/align/splign/Makefile.xalgoalignsplign.lib b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+index d67680b..3d56789 100644
+--- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib
++++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+@@ -10,3 +10,5 @@ LIB = xalgoalignsplign
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
++
++DLL_LIB = access align_format blastinput dbapi_driver gene_info general seq seqdb xalgoalignnw xalgoalignutil xalgoseq xblast xncbi xobjmgr xobjutil xser xutil # axf prosplign
 diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib
-index 073973b..3be07ae 100644
+index 073973b..c6a4c2c 100644
 --- a/src/algo/blast/api/Makefile.xblast.lib
 +++ b/src/algo/blast/api/Makefile.xblast.lib
 @@ -78,7 +78,7 @@ SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
@@ -147,12 +226,12 @@ index 073973b..3be07ae 100644
  LIB = xblast
  
 -DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
++DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
  
  CFLAGS   = $(FAST_CFLAGS)
  # Strict gcc flags
 diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib
-index bfb315c..6f56c5a 100644
+index bfb315c..2cd809a 100644
 --- a/src/algo/blast/blastinput/Makefile.blastinput.lib
 +++ b/src/algo/blast/blastinput/Makefile.blastinput.lib
 @@ -24,7 +24,7 @@ SRC  = $(SRC_CXX)
@@ -160,7 +239,7 @@ index bfb315c..6f56c5a 100644
  LIB = blastinput
  
 -DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = seqdb ncbi_xloader_blastdb $(OBJMGR_LIBS)
++DLL_LIB = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi
  
  # should be redundant, given the above :-/
  ASN_DEP = seqset xnetblast
@@ -174,8 +253,49 @@ index 8e889a7..1326aee 100644
  WATCHERS = coulouri maning madden camacho
 +
 +DLL_LIB = xutil
+diff --git a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+index fcfb9f9..0e762b4 100644
+--- a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -14,3 +14,5 @@ LDFLAGS  = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+ 
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver seq seqdb seqset xncbi xobjmgr xobjread xobjutil xser xutil # axf
+diff --git a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+index e64f111..475f4a1 100644
+--- a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
++++ b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+@@ -10,3 +10,5 @@ LDFLAGS  = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+ 
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver xncbi xobjmgr # axf
+diff --git a/src/algo/blast/format/Makefile.xblastformat.lib b/src/algo/blast/format/Makefile.xblastformat.lib
+index f7da067..9920332 100644
+--- a/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,6 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ 
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = blastxml xhtml xcgi align_format general scoremat seq seqdb xalnmgr xblast xnetblast xobjmgr xobjutil blast_services ncbi_xloader_genbank xcgi # cobalt
+ 
+ WATCHERS = jianye zaretska madden camacho fongah2
+diff --git a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+index 316d4fa..844de85 100644
+--- a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
++++ b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+@@ -11,3 +11,4 @@ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+ WATCHERS = boratyng madden camacho
+ 
++DLL_LIB = dbapi_driver xncbi xutil # axf
 diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib
-index e618f67..32905ca 100644
+index e618f67..b406cc5 100644
 --- a/src/algo/cobalt/Makefile.cobalt.lib
 +++ b/src/algo/cobalt/Makefile.cobalt.lib
 @@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb
@@ -183,9 +303,41 @@ index e618f67..32905ca 100644
  CXXFLAGS  = $(FAST_CXXFLAGS)
  LDFLAGS = $(FAST_LDFLAGS)
 +
-+DLL_LIB = align_format
++DLL_LIB = align_format dbapi_driver general igblast seq seqdb seqset xalgoalignnw xalgophytree xblast xncbi xnetblast xobjmgr xobjutil xser fastme # axf
+diff --git a/src/algo/dustmask/Makefile.xalgodustmask.lib b/src/algo/dustmask/Makefile.xalgodustmask.lib
+index 84e2568..3632356 100644
+--- a/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -11,3 +11,4 @@ SRC = symdust
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = dbapi_driver seq xncbi xobjmgr # axf
+diff --git a/src/algo/gnomon/Makefile.gnomon.lib b/src/algo/gnomon/Makefile.gnomon.lib
+index af363c0..3235647 100644
+--- a/src/algo/gnomon/Makefile.gnomon.lib
++++ b/src/algo/gnomon/Makefile.gnomon.lib
+@@ -6,7 +6,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) \
+     gnomon_engine gnomon_objmgr score gnomon_model parse hmm gnomon_seq asn1 chainer id_handler \
+     annot select_alignments_alt
+ LIB = xalgognomon
+-DLL_LIB = xobjutil $(SOBJMGR_LIBS)
++DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+diff --git a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+index 686dd70..98f57b2 100644
+--- a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
++++ b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+@@ -2,3 +2,5 @@ WATCHERS = lewisg slottad
+ 
+ LIB = pepXML
+ SRC = pepXML__ pepXML___
++
++DLL_LIB = access align_format dbapi_driver xncbi xser # axf
 diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib
-index 872b92e..24fcff3 100644
+index 872b92e..78261eb 100644
 --- a/src/algo/ms/omssa/Makefile.xomssa.lib
 +++ b/src/algo/ms/omssa/Makefile.xomssa.lib
 @@ -19,3 +19,5 @@ LIB = xomssa
@@ -193,9 +345,51 @@ index 872b92e..24fcff3 100644
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
 +
-+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast
++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp
+diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib
+index 5964ef4..8163366 100644
+--- a/src/algo/phy_tree/Makefile.xalgophytree.lib
++++ b/src/algo/phy_tree/Makefile.xalgophytree.lib
+@@ -6,7 +6,7 @@ ASN_DEP = biotree
+ 
+ SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc
+ LIB = xalgophytree
+-DLL_LIB = biotree
++DLL_LIB = biotree seq xalnmgr xobjutil # fastme
+ 
+ # The -I flag is necessary because filenames in #line directives throw
+ # off some compilers (GCC 2.95 at least). :-/
+diff --git a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+index 15d7440..fab9207 100644
+--- a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
++++ b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+@@ -10,3 +10,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
+ ASN_DEP = biotree seqset taxon1
+ 
+ WATCHERS = boratyng
++
++DLL_LIB = access align_format biotree dbapi_driver fastme gene_info seq taxon1 xalgophytree xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/segmask/Makefile.xalgosegmask.lib b/src/algo/segmask/Makefile.xalgosegmask.lib
+index bd011c1..97281ec 100644
+--- a/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -11,3 +11,4 @@ SRC = segmask
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = align_format xobjmgr
+diff --git a/src/algo/seqqa/Makefile.xalgoseqqa.lib b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+index b1bea47..a0e5b1b 100644
+--- a/src/algo/seqqa/Makefile.xalgoseqqa.lib
++++ b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+@@ -12,3 +12,5 @@ LIB = xalgoseqqa
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
++
++DLL_LIB = access align_format dbapi_driver entrez2cli gene_info general seq seqtest xalgognomon xalgoseq xalnmgr xncbi xobjmgr xobjutil xser # axf
 diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib
-index 51f4cd7..0c20790 100644
+index 51f4cd7..724e939 100644
 --- a/src/algo/sequence/Makefile.xalgoseq.lib
 +++ b/src/algo/sequence/Makefile.xalgoseq.lib
 @@ -13,3 +13,5 @@ LDFLAGS  = $(FAST_LDFLAGS)
@@ -203,7 +397,30 @@ index 51f4cd7..0c20790 100644
  
  WATCHERS = dicuccio
 +
-+DLL_LIB = taxon1 xalnmgr
++DLL_LIB = taxon1 xalnmgr xregexp align_format seqset xobjmgr xobjutil
+diff --git a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+index 5562f82..68d3a87 100644
+--- a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
++++ b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+@@ -24,3 +24,6 @@ SRC =   RowSelector \
+         RefinerTrial \
+         RefinerEngine \
+         Interface
++
++DLL_LIB = blastinput cdd ncbi_xcache_bdb xcd_utils xncbi xser xutil
++
+diff --git a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+index eda71f8..8d3a96a 100644
+--- a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
++++ b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+@@ -68,6 +68,6 @@ SRC = \
+     cuTaxTree \
+     cuUtils
+ 
+-DLL_LIB = xobjread
++DLL_LIB = xobjread blastdb blast_services cdd entrez2cli id1cli mmdb ncbimime scoremat taxon1 xblast xobjmgr xregexp
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
 diff --git a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
 index 676a8dd..3d3e4c9 100644
 --- a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
@@ -234,15 +451,36 @@ index c06a2c0..9f1ff25 100644
  LIB = xstruct_thread
 +
 +DLL_LIB = xutil
+diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib
+index 81ba0e6..f25073e 100644
+--- a/src/algo/text/Makefile.xalgotext.lib
++++ b/src/algo/text/Makefile.xalgotext.lib
+@@ -10,3 +10,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+ ASN_DEP = general
++
++DLL_LIB = align_format blastinput ncbi_xcache_bdb xcompress xncbi xutil # axf
+diff --git a/src/algo/volume_merge/Makefile.xalgovmerge.lib b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+index 499861a..3ffb80b 100644
+--- a/src/algo/volume_merge/Makefile.xalgovmerge.lib
++++ b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+@@ -10,3 +10,5 @@ SRC = volume_merge
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++
++DLL_LIB = xncbi
 diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib
-index afaf676..7344871 100644
+index afaf676..ad2c1fe 100644
 --- a/src/algo/winmask/Makefile.xalgowinmask.lib
 +++ b/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+@@ -21,3 +21,5 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
-+DLL_LIB = seqmasks_io
++DLL_LIB = seqmasks_io  xobjread xobjutil
++
 diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib
 index a990390..edf40aa 100644
 --- a/src/cgi/Makefile.cgi.lib
@@ -479,6 +717,26 @@ index a57c1e3..0005299 100644
  WATCHERS = ivanov
 +
 +DLL_LIB = xncbi xutil
+diff --git a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+index 6d7a4af..332e5d0 100644
+--- a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
++++ b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+@@ -7,3 +7,5 @@ SRC = redirect
+ LIB = xcgi_redirect
+ 
+ WATCHERS = ivanov
++
++DLL_LIB = axf dbapi_driver xcgi xhtml xncbi
+diff --git a/src/misc/grid_cgi/Makefile.xgridcgi.lib b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+index c9ef138..8e25cbe 100644
+--- a/src/misc/grid_cgi/Makefile.xgridcgi.lib
++++ b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+@@ -9,3 +9,5 @@ LIB = xgridcgi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+ 
+ WATCHERS = vakatov
++
++DLL_LIB = xncbi xcgi xconnserv xhtml
 diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib
 index 11421d9..e7900a1 100644
 --- a/src/objects/access/Makefile.access.lib
@@ -545,14 +803,14 @@ index d18eb78..f90501d 100644
 +
 +DLL_LIB = xser
 diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib
-index 978cae9..2365261 100644
+index 978cae9..24b726c 100644
 --- a/src/objects/cdd/Makefile.cdd.lib
 +++ b/src/objects/cdd/Makefile.cdd.lib
 @@ -1,2 +1,4 @@
  LIB = cdd
  SRC = cdd__ cdd___
 +
-+DLL_LIB = mmdb xser scoremat
++DLL_LIB = mmdb xser scoremat cn3d
 diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib
 index 1af5d1d..ecd31b2 100644
 --- a/src/objects/cn3d/Makefile.cn3d.lib
@@ -1006,8 +1264,18 @@ index 90eeee0..138e836 100644
  WATCHERS = ucko vasilche
  
 +DLL_LIB = xser xobjmgr
+diff --git a/src/objtools/align/Makefile.xalntool.lib b/src/objtools/align/Makefile.xalntool.lib
+index cb9846d..9c2a8f9 100644
+--- a/src/objtools/align/Makefile.xalntool.lib
++++ b/src/objtools/align/Makefile.xalntool.lib
+@@ -6,3 +6,5 @@ ASN_DEP = seqset
+ 
+ LIB = xalntool
+ SRC = alngraphic
++
++DLL_LIB = access dbapi_driver general seq xhtml xncbi xobjmgr xobjutil xser # align_format axf blastinput
 diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib
-index 4b3e59e..d8e9345 100644
+index 4b3e59e..c67c352 100644
 --- a/src/objtools/align_format/Makefile.align_format.lib
 +++ b/src/objtools/align_format/Makefile.align_format.lib
 @@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -1015,18 +1283,18 @@ index 4b3e59e..d8e9345 100644
  
  WATCHERS = zaretska jianye madden camacho
 +
-+DLL_LIB = seqdb blastdb xser
++DLL_LIB = seqdb blastdb xser xhtml gene_info xnetblast blast_services ncbi_xloader_genbank xalnmgr xcgi xobjread xobjutil
 diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib
-index e32c351..1702b90 100644
+index e32c351..41355ff 100644
 --- a/src/objtools/alnmgr/Makefile.alnmgr.lib
 +++ b/src/objtools/alnmgr/Makefile.alnmgr.lib
 @@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial	\
  
  WATCHERS = todorov dicuccio grichenk
  
-+DLL_LIB = tables
++DLL_LIB = tables dbapi_driver ncbi_xcache_bdb seq seqset sequtil xncbi xobjmgr xobjutil xser # align_format axf
 diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-index d8177ed..f7beead 100644
+index d8177ed..aa4d8e4 100644
 --- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
 +++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
 @@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -1034,7 +1302,7 @@ index d8177ed..f7beead 100644
  #
  # LIB_OR_DLL = dll
 +
-+DLL_LIB = xncbi xser xobjutil seq
++DLL_LIB = xncbi xser xobjutil seq seqdb
 diff --git a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
 index bf5fd1b..c32aca4 100644
 --- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
@@ -1084,6 +1352,29 @@ index 10a878c..7a70b22 100644
  LDFLAGS  = $(FAST_LDFLAGS)
  
 +DLL_LIB = xncbi xser xnetblast xnetblastcli
+diff --git a/src/objtools/cddalignview/Makefile.cddalignview.lib b/src/objtools/cddalignview/Makefile.cddalignview.lib
+index 8e39baa..f4d3a35 100644
+--- a/src/objtools/cddalignview/Makefile.cddalignview.lib
++++ b/src/objtools/cddalignview/Makefile.cddalignview.lib
+@@ -11,3 +11,5 @@ SRC = \
+ 	cav_seqset
+ 
+ LIB = xcddalignview
++
++DLL_LIB = cdd dbapi_driver general ncbimime seq seqset xncbi xser # align_format axf ncbi_xloader_bam
+diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib
+index 663d755..ad7b3cf 100644
+--- a/src/objtools/cleanup/Makefile.cleanup.lib
++++ b/src/objtools/cleanup/Makefile.cleanup.lib
+@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \
+       cleanup_utils \
+       newcleanupp
+ 
+-DLL_LIB = xregexp $(PCRE_LIB)      
++DLL_LIB = xregexp $(PCRE_LIB) access biblio general pub seq seqset sequtil submit xobjmgr xobjutil xser
+ LIB = xcleanup
+ 
+ LIBS = $(PCRE_LIBS)
 diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
 index 80af69f..704ed7a 100644
 --- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
@@ -1095,6 +1386,26 @@ index 80af69f..704ed7a 100644
 +
 +DLL_LIB = seqdb
 +
+diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+index 80abb48..2ddec92 100644
+--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -6,3 +6,5 @@ SRC = bdbloader_rmt remote_blastdb_adapter
+ ASN_DEP = blastdb xnetblast
+ 
+ WATCHERS = camacho
++
++DLL_LIB = blast_services ncbi_xloader_blastdb xobjmgr
+diff --git a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+index a51042b..fa92fc9 100644
+--- a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
++++ b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_cdd
+ SRC = cdd
+ 
+ ASN_DEP = seqset
++
++DLL_LIB = dbapi_driver general seq seqset xconnect xncbi xobjmgr xser # align_format axf ncbi_xloader_bam
 diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 index f2b2b49..864e4b1 100644
 --- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
@@ -1108,7 +1419,7 @@ index f2b2b49..864e4b1 100644
  
  WATCHERS = vasilche
 diff --git a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-index 0a29cbf..015ac93 100644
+index 0a29cbf..74c30dc 100644
 --- a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
 +++ b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
 @@ -15,3 +15,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
@@ -1116,7 +1427,27 @@ index 0a29cbf..015ac93 100644
  
  WATCHERS = vasilche
 +
-+DLL_LIB = xncbi
++DLL_LIB = xncbi gene_info id2 ncbi_xreader xconnect xser
+diff --git a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+index 8d09d8c..d6040ed 100644
+--- a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
++++ b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+@@ -7,3 +7,5 @@ ASN_DEP = seq seqset seqedit
+ 
+ 
+ WATCHERS = vasilche
++
++DLL_LIB = dbapi_driver seq seqedit seqset xncbi xobjmgr xser # axf
+diff --git a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+index d2debd5..33fed34 100644
+--- a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
++++ b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_trace
+ SRC = trace_chgr
+ 
+ ASN_DEP = id1
++
++DLL_LIB = dbapi_driver general id1 id1cli seq xncbi xobjmgr xser # align_format axf
 diff --git a/src/objtools/edit/Makefile.edit.lib b/src/objtools/edit/Makefile.edit.lib
 index 7ce0d11..f5458c5 100644
 --- a/src/objtools/edit/Makefile.edit.lib
@@ -1127,6 +1458,16 @@ index 7ce0d11..f5458c5 100644
  WATCHERS = bollin
 +
 +DLL_LIB = xncbi seq xobjutil xobjmgr
+diff --git a/src/objtools/eutils/api/Makefile.eutils.lib b/src/objtools/eutils/api/Makefile.eutils.lib
+index da71ea9..b444e72 100644
+--- a/src/objtools/eutils/api/Makefile.eutils.lib
++++ b/src/objtools/eutils/api/Makefile.eutils.lib
+@@ -10,3 +10,5 @@ ASN_DEP = einfo esearch egquery epost elink esummary espell uilist \
+           ehistory
+ 
+ WATCHERS = grichenk
++
++DLL_LIB = dbapi_driver xconnect xncbi xser # align_format axf ncbi_xloader_bam
 diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib
 index 82b4ed0..7030a29 100644
 --- a/src/objtools/eutils/egquery/Makefile.egquery.lib
@@ -1217,8 +1558,18 @@ index 19b2b8a..77dcc3c 100644
  WATCHERS = grichenk
 +
 +DLL_LIB = xser
+diff --git a/src/objtools/eutils/uilist/Makefile.uilist.lib b/src/objtools/eutils/uilist/Makefile.uilist.lib
+index b49c3c5..2ee63f0 100644
+--- a/src/objtools/eutils/uilist/Makefile.uilist.lib
++++ b/src/objtools/eutils/uilist/Makefile.uilist.lib
+@@ -4,3 +4,5 @@ SRC = uilist__ uilist___
+ LIB = uilist
+ 
+ WATCHERS = grichenk
++
++DLL_LIB = access dbapi_driver xncbi xser # align_format axf
 diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib
-index a4fc469..0203fea 100644
+index a4fc469..fa58b3c 100644
 --- a/src/objtools/format/Makefile.xformat.lib
 +++ b/src/objtools/format/Makefile.xformat.lib
 @@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \
@@ -1226,7 +1577,7 @@ index a4fc469..0203fea 100644
  
  WATCHERS = ludwigf dicuccio kornbluh
 +
-+DLL_LIB = submit connect xncbi gbseq xobjmgr
++DLL_LIB = submit connect xncbi gbseq xobjmgr xobjutil xalnmgr xconnect
 diff --git a/src/objtools/lds/Makefile.lds.lib b/src/objtools/lds/Makefile.lds.lib
 index e371035..689cfb4 100644
 --- a/src/objtools/lds/Makefile.lds.lib
@@ -1270,6 +1621,18 @@ index 85eefe2..9f317ae 100644
  
 -DLL_LIB = xobjread
 +DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil
+diff --git a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+index 687af1e..f48568c 100644
+--- a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -11,6 +11,6 @@ mask_writer_seqloc \
+ mask_writer_blastdb_maskinfo
+ 
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb blastdb xobjread xobjutil
+ 
+ WATCHERS = morgulis camacho
 diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib
 index dab25d6..f676dc7 100644
 --- a/src/objtools/simple/Makefile.xobjsimple.lib
@@ -1279,6 +1642,16 @@ index dab25d6..f676dc7 100644
  SRC = simple_om
  
 +DLL_LIB = xobjmgr ncbi_xloader_genbank
+diff --git a/src/objtools/snputil/Makefile.snputil.lib b/src/objtools/snputil/Makefile.snputil.lib
+index 15abef3..5ad1560 100644
+--- a/src/objtools/snputil/Makefile.snputil.lib
++++ b/src/objtools/snputil/Makefile.snputil.lib
+@@ -9,3 +9,5 @@ SRC = snp_utils snp_bitfield \
+ ASN_DEP = seqset
+ 
+ WATCHERS = rudnev
++
++DLL_LIB = general seq xncbi xobjmgr xser
 diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib
 index 80a74d8..6eec94b 100644
 --- a/src/objtools/validator/Makefile.validator.lib
@@ -1298,6 +1671,66 @@ index cd6596b..a7d0c01 100644
  WATCHERS = ludwigf boukn
  
 +DLL_LIB = xobjutil xalnmgr
+diff --git a/src/sample/app/asn/Makefile.sample_asn.lib b/src/sample/app/asn/Makefile.sample_asn.lib
+index 0db9ebd..26e6ad9 100644
+--- a/src/sample/app/asn/Makefile.sample_asn.lib
++++ b/src/sample/app/asn/Makefile.sample_asn.lib
+@@ -10,3 +10,5 @@ LIB = sample_asn
+ ASN_DEP = general
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver general xncbi xser
+diff --git a/src/sample/app/soap/Makefile.soap_dataobj.lib b/src/sample/app/soap/Makefile.soap_dataobj.lib
+index 4b87f51..c398ded 100644
+--- a/src/sample/app/soap/Makefile.soap_dataobj.lib
++++ b/src/sample/app/soap/Makefile.soap_dataobj.lib
+@@ -2,3 +2,5 @@ LIB = soap_dataobj
+ SRC = soap_dataobj__ soap_dataobj___
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+index f9d6103..4c22831 100644
+--- a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
++++ b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = asn_sample_lib
+ SRC = asn_sample_lib__ asn_sample_lib___
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/basic/Makefile.basic_sample_lib.lib b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+index a6ba11a..364d9fc 100644
+--- a/src/sample/lib/basic/Makefile.basic_sample_lib.lib
++++ b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+@@ -5,3 +5,5 @@ SRC = basic_sample_lib
+ 
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi
+diff --git a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+index d2a27ef..a63a7e8 100644
+--- a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
++++ b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = dtd_sample_lib
+ SRC = dtd_sample_lib__ dtd_sample_lib___
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+index 4b7b6e2..838e8ea 100644
+--- a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
++++ b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = xsd_sample_lib
+ SRC = xsd_sample_lib__ xsd_sample_lib___
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
 diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib
 index 2563b5f..efad054 100644
 --- a/src/serial/Makefile.serial.lib
@@ -1337,6 +1770,19 @@ index 9877691..599ef5d 100644
  WATCHERS = gouriano
  
 +DLL_LIB = xncbi xutil xser
+diff --git a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+index 4896661..8e2ad56 100644
+--- a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
++++ b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+@@ -12,7 +12,7 @@ ASN_DEP = seqset seq
+ 
+ LIB_OR_DLL = both
+ 
+-DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB)
++DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) xobjreadex
+ LIBS =  $(CMPRS_LIBS) $(ORIG_LIBS)
+ 
+ CPPFLAGS = $(SRA_INCLUDE) -DNCBI_XLOADER_BAM_EXPORTS $(ORIG_CPPFLAGS)
 diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib
 index f2a2f58..f61b25a 100644
 --- a/src/sra/sdk/libs/align/Makefile.align-writer.lib