6 files changed, 173 insertions, 191 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index aefb42e3cd67..3c1ef4e2cf66 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -2,18 +2,20 @@
 # $FreeBSD$
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2009.03.01	# containing BLAST v2.2.19
-PORTREVISION=	1
+PORTVERSION=	2012.06.20	# containing BLAST v2.2.27
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
+MASTER_SITES=	ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
 DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
 
+OPTIONS_DEFINE=	DOCS
+
 USE_MOTIF=	yes
-CPIO_ARGS=	--quiet -pdum -R
+MAKE_JOBS_UNSAFE=	yes
+
 SUB_FILES=	pkg-message
 
 # These are the executables we install.
@@ -28,32 +30,42 @@ SUB_FILES=	pkg-message
 # change in the future with the addition of selectable knobs or
 # new slave ports
 
-TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \
-		debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \
-		idfetch indexpub makeset tbl2asn vecscreen demo_regexp \
-		demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp
+TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
+		checksub debruijn demo_regexp demo_regexp_grep dosimple \
+		entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
+		gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
+		vecscreen
 BLAST_EXE=	bl2seq blastall blastcl3 blastclust blastpgp copymat \
 		fastacmd formatdb formatrpsdb impala makemat megablast \
 		rpsblast seedtop taxblast
 X11_EXE=	Nentrez Psequin ddv entrez2 sbtedit udv
 
 # and these are the man pages we have
-MAN1=	Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \
-	asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \
-	cdscan.1 checksub.1 copymat.1 ddv.1 \
-	debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
-	fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \
-	idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \
-	tbl2asn.1 udv.1 vecscreen.1
-
-MLINKS=	blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
-	blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
-	blast.1 seedtop.1 blast.1 rpsblast.1
+MAN1=		Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
+		asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
+		copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
+		fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
+		getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
+		taxblast.1 tbl2asn.1 udv.1 vecscreen.1
+
+MLINKS=		blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
+		blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
+		blast.1 seedtop.1 blast.1 rpsblast.1 
+
+.include <bsd.port.options.mk>
 
 post-patch:
-	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
-		${WRKSRC}/make/makedis.csh \
-		${WRKSRC}/platform/freebsd.ncbi.mk
+	@${REINPLACE_CMD} -e \
+		's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
+	@${REINPLACE_CMD} -e \
+		'/^NCBI_CC/s|=.*|= ${CC}| ; \
+		 /^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
+		 /^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
+		 s|-I/usr/X11R6/include||g ; \
+		 s|-L/usr/X11R6/lib||g ; \
+		 s|/usr/local|${LOCALBASE}|g ; \
+		 s|-Wl,-Bstatic|| ; \
+		 s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk
 
 # the ncbi-toolkit provides a shell script to drive the build
 # and we use it
@@ -68,36 +80,33 @@ do-install:
 .for blastexe in ${BLAST_EXE}
 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)
 .endfor
-
 .for toolkitexe in ${TOOLKIT_EXE}
 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)
 .endfor
-
 .for x11exe in ${X11_EXE}
 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)
 .endfor
-
 	@${MKDIR} ${PREFIX}/lib/${DISTNAME}
 	(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})
+	@${MKDIR} ${PREFIX}/include/${DISTNAME}
+	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
+		${PREFIX}/include/${DISTNAME})
 	@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
-	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME})
-	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect)
-
+	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
+		${PREFIX}/include/${DISTNAME}/connect)
 .for man in ${MAN1}
-	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)
+	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1)
 .endfor
-
-post-install:
 	@${MKDIR} ${DATADIR}
-	(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})
-
-.if !defined(NOPORTDOCS)
+	(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR})
+.if ${PORT_OPTIONS:MDOCS}
 	@${MKDIR} ${DOCSDIR}
-	(cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
-.endif
-
-.if !defined(BATCH)
-	@ ${CAT} ${PKGMESSAGE}
+	@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
+		(cd ${DOCSDIR} && ${TAR} --unlink -xf -)
+	@${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
+	@${FIND} ${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
+	@${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
 .endif
+	@${CAT} ${PKGMESSAGE}
 
 .include <bsd.port.mk>
diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index c5dfce97e894..8b767a5e8fd1 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -1,2 +1,2 @@
-SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
-SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732
+SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
+SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744
diff --git a/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c b/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c
new file mode 100644
index 000000000000..095c6231ba55
--- /dev/null
+++ b/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c
@@ -0,0 +1,11 @@
+--- corelib/ncbimisc.c.orig
++++ corelib/ncbimisc.c
+@@ -1266,7 +1266,7 @@
+   if (len < 1) return NULL;
+ 
+   rsult = (Nlm_CharPtr) MemNew (len + 3);
+-  if (rsult == NULL) return;
++  if (rsult == NULL) return NULL;
+   tmp = rsult;
+ 
+   for (i = 0; /* local [i] != NULL */ i < numitems; i++) {
diff --git a/biology/ncbi-toolkit/files/patch-make-makenet.unx b/biology/ncbi-toolkit/files/patch-make-makenet.unx
index 76d817d6c913..878c36e2abc9 100644
--- a/biology/ncbi-toolkit/files/patch-make-makenet.unx
+++ b/biology/ncbi-toolkit/files/patch-make-makenet.unx
@@ -8,7 +8,7 @@
  SEQUIN_OPTS =
  LIBCOPY = cp -p
  SRCCOPY = ./ln-if-absent
-@@ -923,17 +924,17 @@
+@@ -934,17 +935,17 @@
  	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
  	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
  	$(LIBCOMPADJ) $(LIB2) $(LIB1) \
@@ -17,19 +17,19 @@
  
  udv    : $(OBJUDV)
  	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
-     $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
+ 	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
  	$(LIB23) $(LIBCOMPADJ) $(LIB2) \
 -	$(LIB1) $(VIBLIBS) $(OTHERLIBS)
 +	$(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
  
  Nentrez : entrez.c $(ULIB31)
  	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
--    $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
-+    $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
+-	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
++	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
  
  # left this in (Tentrez) for script backwards compatibility
  Tentrez : entrez.c $(ULIB31)
-@@ -1114,7 +1115,7 @@
+@@ -1140,7 +1141,7 @@
  entrez2 :	entrez2.c
  	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
  		$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
@@ -38,7 +38,7 @@
  	$(VIB_POST_LINK) entrez2
  
  # demo program (spidey)
-@@ -1383,7 +1384,7 @@
+@@ -1421,7 +1422,7 @@
  	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
  	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
  	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
@@ -47,7 +47,7 @@
  	$(VIB_POST_LINK) Psequin
  
  # 'sbtedit' Submission Template Editor
-@@ -1395,7 +1396,7 @@
+@@ -1433,7 +1434,7 @@
  	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
  	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
  	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
@@ -55,4 +55,4 @@
 +	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
  	$(VIB_POST_LINK) sbtedit
  
- salogif.o:	salogif.c
+ # 'streamer' Sequinesque Stream Editor
diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr
index 626926daca04..35331ba63d4d 100644
--- a/biology/ncbi-toolkit/pkg-descr
+++ b/biology/ncbi-toolkit/pkg-descr
@@ -16,4 +16,4 @@ From the README:
   have found it a useful and stable basis for a number of tools and
   applications.
 
-WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
+WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index 6804d8608983..6388a9c0dcb8 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -1,87 +1,51 @@
-bin/bl2seq
-bin/blastall
-bin/blastcl3
-bin/blastclust
-bin/blastpgp
-bin/copymat
-bin/fastacmd
-bin/formatdb
-bin/formatrpsdb
-bin/impala
-bin/makemat
-bin/megablast
-bin/rpsblast
-bin/seedtop
-bin/taxblast
+bin/Nentrez
+bin/Psequin
 bin/asn2ff
 bin/asn2gb
 bin/asn2idx
 bin/asn2xml
 bin/asndhuff
 bin/asntool
+bin/bl2seq
+bin/blastall
+bin/blastcl3
+bin/blastclust
+bin/blastpgp
+bin/cdscan
 bin/checksub
+bin/copymat
+bin/ddv
 bin/debruijn
+bin/demo_regexp
+bin/demo_regexp_grep
+bin/dosimple
 bin/entrcmd
+bin/entrez2
+bin/errhdr
 bin/fa2htgs
+bin/fastacmd
 bin/findspl
+bin/formatdb
+bin/formatrpsdb
+bin/gene2xml
 bin/getmesh
 bin/getpub
-bin/ddv
 bin/gil2bin
 bin/idfetch
+bin/impala
 bin/indexpub
+bin/makemat
 bin/makeset
-bin/tbl2asn
-bin/vecscreen
-bin/demo_regexp
-bin/demo_regexp_grep
-bin/errhdr
-bin/gene2xml
+bin/megablast
 bin/ncbisort
-bin/seqtest
-bin/test_regexp
-bin/Nentrez
-bin/Psequin
-bin/entrez2
+bin/rpsblast
 bin/sbtedit
+bin/seedtop
+bin/seqtest
+bin/taxblast
+bin/tbl2asn
 bin/udv
-include/ncbi/connect/connect_export.h
-include/ncbi/connect/ncbi_ansi_ext.h
-include/ncbi/connect/ncbi_assert.h
-include/ncbi/connect/ncbi_buffer.h
-include/ncbi/connect/ncbi_comm.h
-include/ncbi/connect/ncbi_config.h
-include/ncbi/connect/ncbi_connection.h
-include/ncbi/connect/ncbi_connector.h
-include/ncbi/connect/ncbi_connssl.h
-include/ncbi/connect/ncbi_connutil.h
-include/ncbi/connect/ncbi_core.h
-include/ncbi/connect/ncbi_core_c.h
-include/ncbi/connect/ncbi_dispd.h
-include/ncbi/connect/ncbi_file_connector.h
-include/ncbi/connect/ncbi_ftp_connector.h
-include/ncbi/connect/ncbi_gnutls.h
-include/ncbi/connect/ncbi_heapmgr.h
-include/ncbi/connect/ncbi_host_info.h
-include/ncbi/connect/ncbi_host_infop.h
-include/ncbi/connect/ncbi_http_connector.h
-include/ncbi/connect/ncbi_lb.h
-include/ncbi/connect/ncbi_lbsmd.h
-include/ncbi/connect/ncbi_local.h
-include/ncbi/connect/ncbi_memory_connector.h
-include/ncbi/connect/ncbi_priv.h
-include/ncbi/connect/ncbi_sendmail.h
-include/ncbi/connect/ncbi_server_info.h
-include/ncbi/connect/ncbi_server_infop.h
-include/ncbi/connect/ncbi_service.h
-include/ncbi/connect/ncbi_service_connector.h
-include/ncbi/connect/ncbi_servicep.h
-include/ncbi/connect/ncbi_socket.h
-include/ncbi/connect/ncbi_socket_connector.h
-include/ncbi/connect/ncbi_socket_unix.h
-include/ncbi/connect/ncbi_socketp.h
-include/ncbi/connect/ncbi_types.h
-include/ncbi/connect/ncbi_util.h
+bin/vecscreen
 include/ncbi/FSpCompat.h
 include/ncbi/FullPath.h
 include/ncbi/MoreCarbonAccessors.h
@@ -155,6 +119,7 @@ include/ncbi/asntax1.h
 include/ncbi/asntax3.h
 include/ncbi/asntaxon.h
 include/ncbi/asntseq.h
+include/ncbi/asnvalid.h
 include/ncbi/bandalgn.h
 include/ncbi/binary.h
 include/ncbi/biosrc.h
@@ -185,7 +150,6 @@ include/ncbi/cdrom.h
 include/ncbi/cdromlib.h
 include/ncbi/cn3d.h
 include/ncbi/cn3dentr.h
-include/ncbi/codon.h
 include/ncbi/cn3dmain.h
 include/ncbi/cn3dmesh.h
 include/ncbi/cn3dmodl.h
@@ -196,10 +160,50 @@ include/ncbi/cn3dsave.h
 include/ncbi/cn3dshim.h
 include/ncbi/cn3dstyl.h
 include/ncbi/cn3dxprt.h
+include/ncbi/codon.h
 include/ncbi/compo_heap.h
 include/ncbi/compo_mode_condition.h
 include/ncbi/composition_adjustment.h
 include/ncbi/composition_constants.h
+include/ncbi/connect/connect_export.h
+include/ncbi/connect/ncbi_ansi_ext.h
+include/ncbi/connect/ncbi_assert.h
+include/ncbi/connect/ncbi_base64.h
+include/ncbi/connect/ncbi_buffer.h
+include/ncbi/connect/ncbi_comm.h
+include/ncbi/connect/ncbi_config.h
+include/ncbi/connect/ncbi_connection.h
+include/ncbi/connect/ncbi_connector.h
+include/ncbi/connect/ncbi_connssl.h
+include/ncbi/connect/ncbi_connutil.h
+include/ncbi/connect/ncbi_core.h
+include/ncbi/connect/ncbi_core_c.h
+include/ncbi/connect/ncbi_dispd.h
+include/ncbi/connect/ncbi_file_connector.h
+include/ncbi/connect/ncbi_ftp_connector.h
+include/ncbi/connect/ncbi_gnutls.h
+include/ncbi/connect/ncbi_heapmgr.h
+include/ncbi/connect/ncbi_host_info.h
+include/ncbi/connect/ncbi_host_infop.h
+include/ncbi/connect/ncbi_http_connector.h
+include/ncbi/connect/ncbi_lb.h
+include/ncbi/connect/ncbi_lbsmd.h
+include/ncbi/connect/ncbi_local.h
+include/ncbi/connect/ncbi_memory_connector.h
+include/ncbi/connect/ncbi_priv.h
+include/ncbi/connect/ncbi_sendmail.h
+include/ncbi/connect/ncbi_server_info.h
+include/ncbi/connect/ncbi_server_infop.h
+include/ncbi/connect/ncbi_service.h
+include/ncbi/connect/ncbi_service_connector.h
+include/ncbi/connect/ncbi_servicep.h
+include/ncbi/connect/ncbi_socket.h
+include/ncbi/connect/ncbi_socket_connector.h
+include/ncbi/connect/ncbi_socket_unix.h
+include/ncbi/connect/ncbi_socketp.h
+include/ncbi/connect/ncbi_types.h
+include/ncbi/connect/ncbi_util.h
+include/ncbi/connect/ncbi_version.h
 include/ncbi/corematx.h
 include/ncbi/db_list.h
 include/ncbi/ddvclick.h
@@ -240,12 +244,12 @@ include/ncbi/gather.h
 include/ncbi/gbfeat.h
 include/ncbi/gbftdef.h
 include/ncbi/gbparlex.h
-include/ncbi/id1.h
 include/ncbi/gifgen.h
 include/ncbi/glbpic.h
 include/ncbi/gphdraw.h
 include/ncbi/gtrdraw.h
 include/ncbi/gxydraw.h
+include/ncbi/id1.h
 include/ncbi/id1arch.h
 include/ncbi/id1gen.h
 include/ncbi/id1map.h
@@ -289,9 +293,9 @@ include/ncbi/medutil.h
 include/ncbi/medview.h
 include/ncbi/mimapi.h
 include/ncbi/mkbioseq.h
-include/ncbi/mmdb1.h
 include/ncbi/mla2api.h
 include/ncbi/mlkludge.h
+include/ncbi/mmdb1.h
 include/ncbi/mmdb2.h
 include/ncbi/mmdb3.h
 include/ncbi/mmdbapi.h
@@ -303,6 +307,7 @@ include/ncbi/mmdbdata.h
 include/ncbi/mmdblocl.h
 include/ncbi/motif.h
 include/ncbi/ncbi.h
+include/ncbi/ncbi_skew_guard.h
 include/ncbi/ncbibs.h
 include/ncbi/ncbidraw.h
 include/ncbi/ncbienv.h
@@ -338,11 +343,8 @@ include/ncbi/netentr.h
 include/ncbi/netlib.h
 include/ncbi/netpriv.h
 include/ncbi/netscape.h
-include/ncbi/ni_defin.h
 include/ncbi/ni_error.h
-include/ncbi/ni_lib.h
 include/ncbi/ni_lib_.h
-include/ncbi/ni_net.h
 include/ncbi/ni_types.h
 include/ncbi/nlm_linear_algebra.h
 include/ncbi/objacces.h
@@ -392,6 +394,7 @@ include/ncbi/objtable.h
 include/ncbi/objtax1.h
 include/ncbi/objtax3.h
 include/ncbi/objtseq.h
+include/ncbi/objvalid.h
 include/ncbi/odlbox.h
 include/ncbi/optimize_target_freq.h
 include/ncbi/panels.h
@@ -478,7 +481,6 @@ include/ncbi/suggen.h
 include/ncbi/suggest.h
 include/ncbi/suggslp.h
 include/ncbi/sugmap.h
-include/ncbi/terr.h
 include/ncbi/sugprefx.h
 include/ncbi/tax1map.h
 include/ncbi/tax3api.h
@@ -488,6 +490,7 @@ include/ncbi/taxinc.h
 include/ncbi/taxon1.h
 include/ncbi/taxuerr.h
 include/ncbi/taxutil.h
+include/ncbi/terr.h
 include/ncbi/tfuns.h
 include/ncbi/thrdatd.h
 include/ncbi/thrddecl.h
@@ -523,6 +526,8 @@ include/ncbi/urkutil.h
 include/ncbi/urlquery.h
 include/ncbi/utilpars.h
 include/ncbi/utilpub.h
+include/ncbi/valapi.h
+include/ncbi/valdlg.h
 include/ncbi/valid.h
 include/ncbi/validatr.h
 include/ncbi/validerr.h
@@ -531,7 +536,6 @@ include/ncbi/vast2mage.h
 include/ncbi/vast2pdb.h
 include/ncbi/vastlocl.h
 include/ncbi/vastsrv.h
-include/ncbi/vsm.h
 include/ncbi/vecscnapi.h
 include/ncbi/vecscrn.h
 include/ncbi/vibdefns.h
@@ -551,6 +555,7 @@ include/ncbi/viewer.h
 include/ncbi/viewer3d.h
 include/ncbi/viewerp.h
 include/ncbi/viewmgr.h
+include/ncbi/vsm.h
 include/ncbi/vsmfile.h
 include/ncbi/vsmpriv.h
 include/ncbi/vsmutil.h
@@ -586,10 +591,10 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/access.txt
 %%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
 %%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/blast.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/blastall.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/blastdb.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/blastftp.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/blastpgp.html
@@ -613,7 +618,6 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/firewall.html
 %%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh
 %%PORTDOCS%%%%DOCSDIR%%/gene2xml.txt
-%%PORTDOCS%%%%DOCSDIR%%/images/logo.png
 %%PORTDOCS%%%%DOCSDIR%%/images/affil.png
 %%PORTDOCS%%%%DOCSDIR%%/images/annot.png
 %%PORTDOCS%%%%DOCSDIR%%/images/authors.png
@@ -624,6 +628,7 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/images/genbank.png
 %%PORTDOCS%%%%DOCSDIR%%/images/graphic.png
 %%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png
+%%PORTDOCS%%%%DOCSDIR%%/images/logo.png
 %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
 %%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png
 %%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png
@@ -639,67 +644,11 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/images/update.png
 %%PORTDOCS%%%%DOCSDIR%%/images/validate.png
 %%PORTDOCS%%%%DOCSDIR%%/images/welcome.png
-%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2all.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2fsa.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2idx.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asnval.1
-%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blast.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blastall.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blastall_old.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1
-%%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1
-%%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1
-%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1
-%%PORTDOCS%%%%DOCSDIR%%/man/cleanasn.1
-%%PORTDOCS%%%%DOCSDIR%%/man/copymat.1
-%%PORTDOCS%%%%DOCSDIR%%/man/ddv.1
-%%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1
-%%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1
-%%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
-%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1
-%%PORTDOCS%%%%DOCSDIR%%/man/fa2htgs.1
-%%PORTDOCS%%%%DOCSDIR%%/man/fastacmd.1
-%%PORTDOCS%%%%DOCSDIR%%/man/findspl.1
-%%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1
-%%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1
-%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1
-%%PORTDOCS%%%%DOCSDIR%%/man/formatrpsdb.1
-%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1
-%%PORTDOCS%%%%DOCSDIR%%/man/gene2xml.1
-%%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1
-%%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1
-%%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1
-%%PORTDOCS%%%%DOCSDIR%%/man/impala.1
-%%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1
-%%PORTDOCS%%%%DOCSDIR%%/man/insdseqget.1
-%%PORTDOCS%%%%DOCSDIR%%/man/makemat.1
-%%PORTDOCS%%%%DOCSDIR%%/man/makeset.1
-%%PORTDOCS%%%%DOCSDIR%%/man/megablast.1
-%%PORTDOCS%%%%DOCSDIR%%/man/nps2gps.1
-%%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1
-%%PORTDOCS%%%%DOCSDIR%%/man/sbtedit.1
-%%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1
-%%PORTDOCS%%%%DOCSDIR%%/man/sortbyquote.1
-%%PORTDOCS%%%%DOCSDIR%%/man/spidey.1
-%%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1
-%%PORTDOCS%%%%DOCSDIR%%/man/trna2sap.1
-%%PORTDOCS%%%%DOCSDIR%%/man/trna2tbl.1
-%%PORTDOCS%%%%DOCSDIR%%/man/udv.1
 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt
 %%PORTDOCS%%%%DOCSDIR%%/sdk.doc
-%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif
-%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.xml
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css
@@ -709,12 +658,12 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.html
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.html
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.xml
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_install.html
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.html
-%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.xml
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.css
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.html
@@ -726,6 +675,7 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css
@@ -736,6 +686,12 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/16SCore.nhr
 %%DATADIR%%/16SCore.nin
 %%DATADIR%%/16SCore.nsq
+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nhr
+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nin
+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nsq
+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nhr
+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nin
+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nsq
 %%DATADIR%%/BLOSUM45
 %%DATADIR%%/BLOSUM50
 %%DATADIR%%/BLOSUM62
@@ -752,7 +708,6 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/KSchoth.flt
 %%DATADIR%%/KSesigc.mat
 %%DATADIR%%/KSesigl.mat
-%%DATADIR%%/PAM250
 %%DATADIR%%/KSgc.flt
 %%DATADIR%%/KShopp.flt
 %%DATADIR%%/KSkyte.flt
@@ -768,6 +723,7 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/LSURef_93.fasta.nhr
 %%DATADIR%%/LSURef_93.fasta.nin
 %%DATADIR%%/LSURef_93.fasta.nsq
+%%DATADIR%%/PAM250
 %%DATADIR%%/PAM30
 %%DATADIR%%/PAM70
 %%DATADIR%%/SSURef_93.fasta.nhr
@@ -780,6 +736,7 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/UniVec_Core.nin
 %%DATADIR%%/UniVec_Core.nsq
 %%DATADIR%%/asn2ff.prt
+%%DATADIR%%/autofix.prt
 %%DATADIR%%/blast.prt
 %%DATADIR%%/bstdt.prt
 %%DATADIR%%/bstdt.val
@@ -794,6 +751,9 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/gc.val
 %%DATADIR%%/humrep.fsa
 %%DATADIR%%/institution_codes.txt
+%%DATADIR%%/lat_lon_country.txt
+%%DATADIR%%/lat_lon_island.txt
+%%DATADIR%%/lat_lon_water.txt
 %%DATADIR%%/lineages.txt
 %%DATADIR%%/makerpt.prt
 %%DATADIR%%/ncbiendo.dat
@@ -802,6 +762,8 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/ncbiren.dat
 %%DATADIR%%/ncbirnam.dat
 %%DATADIR%%/objprt.prt
+%%DATADIR%%/organelle_products.prt
+%%DATADIR%%/product_rules.prt
 %%DATADIR%%/pubkey.enc
 %%DATADIR%%/rRNA_blast.nal
 %%DATADIR%%/rRNAstrand.nal
@@ -810,13 +772,13 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/sequin.hlp
 %%DATADIR%%/sgmlbb.ent
 %%DATADIR%%/taxlist.txt
-@dirrm include/ncbi/connect
-@dirrm include/ncbi
-@dirrm lib/ncbi
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/man
+%%DATADIR%%/validrules.prt
+@dirrmtry %%DATADIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrmtry %%DATADIR%%
+@dirrm lib/ncbi
+@dirrm include/ncbi/connect
+@dirrm include/ncbi