4 files changed, 276 insertions, 167 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index 81be1572298b..c946237665c1 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2003.04.21
+PORTVERSION=	2004.06.16
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -35,13 +35,13 @@ pre-configure:
 	@${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
 
 post-install:
-	@${MKDIR} ${DATADIR}
+	${MKDIR} ${DATADIR}
 	@for file in ${WRKSRC}/data/*; do \
 		${INSTALL_DATA} $$file ${DATADIR}; \
 	done
 .if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCDIR}
-	@cd ${WRKSRC}/doc && ${FIND} * | \
+	${MKDIR} ${DOCDIR}
+	cd ${WRKSRC}/doc && ${FIND} * | \
 	  ${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR}
 .endif
 	@${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE}
diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index ee90dff3fe66..282f0acf867f 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -1 +1,2 @@
-MD5 (ncbi.tar.gz) = 96208e10f92b2163f5dcc3c5cf74dd44
+MD5 (ncbi.tar.gz) = 12320f853acb397a14729fb0da0b09df
+SIZE (ncbi.tar.gz) = 13680457
diff --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa
index 8bb479ec9b0b..65458348ad2a 100644
--- a/biology/ncbi-toolkit/files/patch-aa
+++ b/biology/ncbi-toolkit/files/patch-aa
@@ -1,6 +1,6 @@
---- make/makeall.unx.orig	Thu Mar 21 06:01:20 2002
-+++ make/makeall.unx	Sat Jun  8 20:16:09 2002
-@@ -859,3 +859,46 @@
+--- make/makeall.unx.orig	Tue Jun  8 17:44:54 2004
++++ make/makeall.unx	Mon Nov  1 21:07:43 2004
+@@ -944,3 +944,48 @@
  	#load $(LDFLAGS) getmuid.c medutil.c \
  	$(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \
  	$(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl
@@ -10,7 +10,7 @@
 +		blastall blastcl3 blastclust blastpgp \
 +		cdscan checksub copymat \
 +		ddv demo_regexp demo_regexp_grep dosimple \
-+		entrcmd entrez2 errhdr fa2htgs fastacmd findspl fmerge formatdb \
++		entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb \
 +		getfeat getmesh getpub getseq gil2bin \
 +		idfetch impala indexpub \
 +		makemat makeset megablast \
@@ -26,7 +26,9 @@
 +
 +binstall: $(EXE)
 +	${MKDIR} ${PREFIX}/bin
-+	${INSTALL_PROGRAM} -s $? /${PREFIX}/bin
++.for f in $(EXE)
++	${INSTALL_PROGRAM} -s $(f) ${PREFIX}/bin
++.endfor
 +
 +linstall: $(LIB)
 +	${MKDIR} ${PREFIX}/lib/ncbi
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index d9cd41b1a767..08b9f8f2544d 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -1,51 +1,3 @@
-%%PORTDOCS%%%%DOCSDIR%%/FAQ.txt
-%%PORTDOCS%%%%DOCSDIR%%/README-qm
-%%PORTDOCS%%%%DOCSDIR%%/README.asn2xml
-%%PORTDOCS%%%%DOCSDIR%%/README.bcl
-%%PORTDOCS%%%%DOCSDIR%%/README.bls
-%%PORTDOCS%%%%DOCSDIR%%/README.fastacmd
-%%PORTDOCS%%%%DOCSDIR%%/README.formatdb
-%%PORTDOCS%%%%DOCSDIR%%/README.imp
-%%PORTDOCS%%%%DOCSDIR%%/README.mbl
-%%PORTDOCS%%%%DOCSDIR%%/README.nbl
-%%PORTDOCS%%%%DOCSDIR%%/README.pbl
-%%PORTDOCS%%%%DOCSDIR%%/README.rps
-%%PORTDOCS%%%%DOCSDIR%%/README.sdk
-%%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
-%%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
-%%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
-%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc
-%%PORTDOCS%%%%DOCSDIR%%/firedialog.gif
-%%PORTDOCS%%%%DOCSDIR%%/firewall.html
-%%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh
-%%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn01.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn02.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn03.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn04.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn05.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn06.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn07.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn08.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn09.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn10.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn11.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn12.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn13.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn14.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn15.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn16.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn17.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn18.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn19.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn20.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn21.gif
-%%PORTDOCS%%%%DOCSDIR%%/images/seqn22.gif
-%%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt
-%%PORTDOCS%%%%DOCSDIR%%/sdk.doc
-%%PORTDOCS%%%%DOCSDIR%%/sequin.htm
-%%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt
 bin/Nentrez
 bin/Psequin
 bin/asn2ff
@@ -70,7 +22,6 @@ bin/errhdr
 bin/fa2htgs
 bin/fastacmd
 bin/findspl
-bin/fmerge
 bin/formatdb
 bin/getfeat
 bin/getmesh
@@ -94,56 +45,6 @@ bin/testobj
 bin/testval
 bin/udv
 bin/vecscreen
-lib/ncbi/libddvlib.a
-lib/ncbi/libncbi.a
-lib/ncbi/libncbiCacc.a
-lib/ncbi/libncbiNacc.a
-lib/ncbi/libncbiacc.a
-lib/ncbi/libncbicdr.a
-lib/ncbi/libncbicn3d.a
-lib/ncbi/libncbidesk.a
-lib/ncbi/libncbiid1.a
-lib/ncbi/libncbimla.a
-lib/ncbi/libncbimmdb.a
-lib/ncbi/libncbiobj.a
-lib/ncbi/libncbitool.a
-lib/ncbi/libncbitxc2.a
-lib/ncbi/libnetblast.a
-lib/ncbi/libnetcli.a
-lib/ncbi/libnetentr.a
-lib/ncbi/libregexp.a
-lib/ncbi/libvibgif.a
-lib/ncbi/libvibnet.a
-lib/ncbi/libvibrant.a
-include/ncbi/connect/connect_export.h
-include/ncbi/connect/ncbi_ansi_ext.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_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_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_lbsmd.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_types.h
-include/ncbi/connect/ncbi_util.h
 include/ncbi/FSpCompat.h
 include/ncbi/FullPath.h
 include/ncbi/MoreCarbonAccessors.h
@@ -175,16 +76,12 @@ include/ncbi/asn2ff.h
 include/ncbi/asn2ff6.h
 include/ncbi/asn2ffg.h
 include/ncbi/asn2ffp.h
+include/ncbi/asn2gnbi.h
 include/ncbi/asn2gnbk.h
 include/ncbi/asn2gnbp.h
 include/ncbi/asn2graphic.h
 include/ncbi/asn2graphicp.h
 include/ncbi/asnacces.h
-include/ncbi/asngbseq.h
-include/ncbi/asntseq.h
-include/ncbi/blast.h
-include/ncbi/blastconcat.h
-include/ncbi/blastconcatdef.h
 include/ncbi/asnalign.h
 include/ncbi/asnbibli.h
 include/ncbi/asnblock.h
@@ -192,8 +89,10 @@ include/ncbi/asncode.h
 include/ncbi/asnent2.h
 include/ncbi/asnfdef.h
 include/ncbi/asnfeat.h
+include/ncbi/asngbseq.h
 include/ncbi/asngen.h
 include/ncbi/asnid0.h
+include/ncbi/asninsdseq.h
 include/ncbi/asnloc.h
 include/ncbi/asnmdrs.h
 include/ncbi/asnmedli.h
@@ -211,9 +110,13 @@ include/ncbi/asnsset.h
 include/ncbi/asnsubmt.h
 include/ncbi/asntax1.h
 include/ncbi/asntaxon.h
+include/ncbi/asntseq.h
 include/ncbi/bandalgn.h
 include/ncbi/binary.h
 include/ncbi/biosrc.h
+include/ncbi/blast.h
+include/ncbi/blastconcat.h
+include/ncbi/blastconcatdef.h
 include/ncbi/blastdef.h
 include/ncbi/blastkar.h
 include/ncbi/blastpat.h
@@ -226,6 +129,7 @@ include/ncbi/bxmlobj.h
 include/ncbi/casn.h
 include/ncbi/cdconfig.h
 include/ncbi/cdd.h
+include/ncbi/cddapi.h
 include/ncbi/cddposutil.h
 include/ncbi/cddsrv.h
 include/ncbi/cddutil.h
@@ -247,6 +151,35 @@ include/ncbi/cn3dshim.h
 include/ncbi/cn3dstyl.h
 include/ncbi/cn3dxprt.h
 include/ncbi/codon.h
+include/ncbi/connect/connect_export.h
+include/ncbi/connect/ncbi_ansi_ext.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_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_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_lbsmd.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_types.h
+include/ncbi/connect/ncbi_util.h
 include/ncbi/corematx.h
 include/ncbi/db_list.h
 include/ncbi/ddvclick.h
@@ -262,9 +195,9 @@ include/ncbi/document.h
 include/ncbi/dotmatrx.h
 include/ncbi/dotseq.h
 include/ncbi/dotviewer.h
-include/ncbi/dust.h
 include/ncbi/drawingp.h
 include/ncbi/drawseq.h
+include/ncbi/dust.h
 include/ncbi/dvncode.h
 include/ncbi/echo_asn.h
 include/ncbi/edutil.h
@@ -296,6 +229,10 @@ include/ncbi/id1.h
 include/ncbi/id1arch.h
 include/ncbi/id1gen.h
 include/ncbi/id1map.h
+include/ncbi/id2.h
+include/ncbi/id2gen.h
+include/ncbi/id2map.h
+include/ncbi/id2sgen.h
 include/ncbi/image.h
 include/ncbi/imagelst.h
 include/ncbi/import.h
@@ -407,6 +344,7 @@ include/ncbi/objfdef.h
 include/ncbi/objfeat.h
 include/ncbi/objgbseq.h
 include/ncbi/objgen.h
+include/ncbi/objinsdseq.h
 include/ncbi/objloc.h
 include/ncbi/objmdrs.h
 include/ncbi/objmedli.h
@@ -424,7 +362,9 @@ include/ncbi/objpub.h
 include/ncbi/objpubd.h
 include/ncbi/objpubme.h
 include/ncbi/objres.h
+include/ncbi/objscoremat.h
 include/ncbi/objseq.h
+include/ncbi/objspell.h
 include/ncbi/objsset.h
 include/ncbi/objsub.h
 include/ncbi/objtax1.h
@@ -452,8 +392,8 @@ include/ncbi/prunebsc.h
 include/ncbi/pubdesc.h
 include/ncbi/puberr.h
 include/ncbi/qblastapi.h
-include/ncbi/regex.h
 include/ncbi/readdb.h
+include/ncbi/regex.h
 include/ncbi/rpsutil.h
 include/ncbi/saldist.h
 include/ncbi/saled.h
@@ -475,6 +415,7 @@ include/ncbi/salstruc.h
 include/ncbi/salutil.h
 include/ncbi/samutil.h
 include/ncbi/satutil.h
+include/ncbi/scoremat.h
 include/ncbi/sdisplay.h
 include/ncbi/sec.h
 include/ncbi/seed.h
@@ -490,12 +431,14 @@ include/ncbi/seqpanel.h
 include/ncbi/seqpcc.h
 include/ncbi/seqport.h
 include/ncbi/seqscrl.h
+include/ncbi/seqsplit.h
 include/ncbi/seqsub.h
 include/ncbi/sequtil.h
 include/ncbi/shim3d.h
 include/ncbi/simple.h
 include/ncbi/simutil.h
 include/ncbi/spell.h
+include/ncbi/spellapi.h
 include/ncbi/spidey.h
 include/ncbi/splutil.h
 include/ncbi/sqnutils.h
@@ -506,7 +449,6 @@ include/ncbi/subutil.h
 include/ncbi/suggapi.h
 include/ncbi/suggen.h
 include/ncbi/suggest.h
-include/ncbi/terr.h
 include/ncbi/suggslp.h
 include/ncbi/sugmap.h
 include/ncbi/sugprefx.h
@@ -517,6 +459,7 @@ 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
@@ -558,7 +501,6 @@ include/ncbi/vast2cn3d.h
 include/ncbi/vast2mage.h
 include/ncbi/vast2pdb.h
 include/ncbi/vastlocl.h
-include/ncbi/vsm.h
 include/ncbi/vastsrv.h
 include/ncbi/vecscnapi.h
 include/ncbi/vecscrn.h
@@ -571,67 +513,231 @@ include/ncbi/vibmouse.h
 include/ncbi/vibpcc.h
 include/ncbi/vibprocs.h
 include/ncbi/vibrant.h
+include/ncbi/vibrgb.h
 include/ncbi/vibtree.h
 include/ncbi/vibtypes.h
 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
 include/ncbi/wrpsb.h
 include/ncbi/wrpsbtool.h
+include/ncbi/wwwblast.h
 include/ncbi/xmlblast.h
-share/ncbi-toolkit/BLOSUM45
-share/ncbi-toolkit/BLOSUM62
-share/ncbi-toolkit/BLOSUM80
-share/ncbi-toolkit/ContactPotential
-share/ncbi-toolkit/KSat.flt
-share/ncbi-toolkit/KSchoth.flt
-share/ncbi-toolkit/KSesigc.mat
-share/ncbi-toolkit/KSesigl.mat
-share/ncbi-toolkit/KSgc.flt
-share/ncbi-toolkit/KShopp.flt
-share/ncbi-toolkit/KSkyte.flt
-share/ncbi-toolkit/KSmtidk.mat
-share/ncbi-toolkit/KSmtk.mat
-share/ncbi-toolkit/KSnsigc.mat
-share/ncbi-toolkit/KSnsigl.mat
-share/ncbi-toolkit/KSpcc.mat
-share/ncbi-toolkit/KSpsigc.mat
-share/ncbi-toolkit/KSpsigl.mat
-share/ncbi-toolkit/KSpur.flt
-share/ncbi-toolkit/KSpyr.flt
-share/ncbi-toolkit/PAM30
-share/ncbi-toolkit/PAM70
-share/ncbi-toolkit/asn2ff.prt
-share/ncbi-toolkit/blast.prt
-share/ncbi-toolkit/bstdt.prt
-share/ncbi-toolkit/bstdt.val
-share/ncbi-toolkit/featdef.prt
-share/ncbi-toolkit/featdef.val
-share/ncbi-toolkit/gc.prt
-share/ncbi-toolkit/gc.val
-share/ncbi-toolkit/humrep.fsa
-share/ncbi-toolkit/lineages.txt
-share/ncbi-toolkit/makerpt.prt
-share/ncbi-toolkit/ncbiendo.dat
-share/ncbi-toolkit/ncbipnam.dat
-share/ncbi-toolkit/ncbipros.dat
-share/ncbi-toolkit/ncbiren.dat
-share/ncbi-toolkit/ncbirnam.dat
-share/ncbi-toolkit/objprt.prt
-share/ncbi-toolkit/pubkey.enc
-share/ncbi-toolkit/seqcode.prt
-share/ncbi-toolkit/seqcode.val
-share/ncbi-toolkit/sequin.hlp
-share/ncbi-toolkit/sgmlbb.ent
-share/ncbi-toolkit/taxlist.txt
-@dirrm include/ncbi/connect
-@dirrm include/ncbi
-@dirrm lib/ncbi
-@dirrm share/ncbi-toolkit
+lib/ncbi/libblast.a
+lib/ncbi/libblastapi.a
+lib/ncbi/libddvlib.a
+lib/ncbi/libncbi.a
+lib/ncbi/libncbiCacc.a
+lib/ncbi/libncbiNacc.a
+lib/ncbi/libncbiacc.a
+lib/ncbi/libncbicdr.a
+lib/ncbi/libncbicn3d.a
+lib/ncbi/libncbidesk.a
+lib/ncbi/libncbiid1.a
+lib/ncbi/libncbimla.a
+lib/ncbi/libncbimmdb.a
+lib/ncbi/libncbiobj.a
+lib/ncbi/libncbitool.a
+lib/ncbi/libncbitxc2.a
+lib/ncbi/libnetblast.a
+lib/ncbi/libnetcli.a
+lib/ncbi/libnetentr.a
+lib/ncbi/libregexp.a
+lib/ncbi/libvibgif.a
+lib/ncbi/libvibnet.a
+lib/ncbi/libvibrant.a
+%%PORTDOCS%%%%DOCSDIR%%/FAQ.txt
+%%PORTDOCS%%%%DOCSDIR%%/README.asn2xml
+%%PORTDOCS%%%%DOCSDIR%%/README.sdk
+%%PORTDOCS%%%%DOCSDIR%%/access.txt
+%%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
+%%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
+%%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
+%%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/filter.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/impala.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/index.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html
+%%PORTDOCS%%%%DOCSDIR%%/blastdb.txt
+%%PORTDOCS%%%%DOCSDIR%%/blastftp.txt
+%%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
+%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
+%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc
+%%PORTDOCS%%%%DOCSDIR%%/firedialog.gif
+%%PORTDOCS%%%%DOCSDIR%%/firewall.html
+%%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh
+%%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn01.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn02.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn03.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn04.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn05.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn06.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn07.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn08.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn09.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn10.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn11.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn12.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn13.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn14.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn15.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn16.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn17.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn18.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn19.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn20.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn21.png
+%%PORTDOCS%%%%DOCSDIR%%/images/seqn22.png
+%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1
+%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1
+%%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1
+%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1
+%%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1
+%%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blastall.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blast.1
+%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1
+%%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1
+%%PORTDOCS%%%%DOCSDIR%%/man/copymat.1
+%%PORTDOCS%%%%DOCSDIR%%/man/ddv.1
+%%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1
+%%PORTDOCS%%%%DOCSDIR%%/man/entrcmd.1
+%%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1
+%%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
+%%PORTDOCS%%%%DOCSDIR%%/man/fastacmd.1
+%%PORTDOCS%%%%DOCSDIR%%/man/fa2htgs.1
+%%PORTDOCS%%%%DOCSDIR%%/man/findspl.1
+%%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1
+%%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1
+%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1
+%%PORTDOCS%%%%DOCSDIR%%/man/getfeat.1
+%%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1
+%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1
+%%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1
+%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1
+%%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1
+%%PORTDOCS%%%%DOCSDIR%%/man/impala.1
+%%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1
+%%PORTDOCS%%%%DOCSDIR%%/man/makemat.1
+%%PORTDOCS%%%%DOCSDIR%%/man/makeset.1
+%%PORTDOCS%%%%DOCSDIR%%/man/megablast.1
+%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1
+%%PORTDOCS%%%%DOCSDIR%%/man/netentcf.1
+%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1
+%%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1
+%%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1
+%%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1
+%%PORTDOCS%%%%DOCSDIR%%/man/udv.1
+%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1
+%%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt
+%%PORTDOCS%%%%DOCSDIR%%/sdk.doc
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF
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+%%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-netscape.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/main.xslt
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/ncbi_sequin.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif
+%%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/seq_mac_download.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.html
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_unix_download.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_unix_download.html
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_unix_download.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie3.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css
+%%PORTDOCS%%%%DOCSDIR%%/sequin.htm
+%%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt
+%%DATADIR%%/BLOSUM45
+%%DATADIR%%/BLOSUM62
+%%DATADIR%%/BLOSUM80
+%%DATADIR%%/ContactPotential
+%%DATADIR%%/KSat.flt
+%%DATADIR%%/KSchoth.flt
+%%DATADIR%%/KSesigc.mat
+%%DATADIR%%/KSesigl.mat
+%%DATADIR%%/KSgc.flt
+%%DATADIR%%/KShopp.flt
+%%DATADIR%%/KSkyte.flt
+%%DATADIR%%/KSmtidk.mat
+%%DATADIR%%/KSmtk.mat
+%%DATADIR%%/KSnsigc.mat
+%%DATADIR%%/KSnsigl.mat
+%%DATADIR%%/KSpcc.mat
+%%DATADIR%%/KSpsigc.mat
+%%DATADIR%%/KSpsigl.mat
+%%DATADIR%%/KSpur.flt
+%%DATADIR%%/KSpyr.flt
+%%DATADIR%%/PAM30
+%%DATADIR%%/PAM70
+%%DATADIR%%/asn2ff.prt
+%%DATADIR%%/blast.prt
+%%DATADIR%%/bstdt.prt
+%%DATADIR%%/bstdt.val
+%%DATADIR%%/featdef.prt
+%%DATADIR%%/featdef.val
+%%DATADIR%%/gc.prt
+%%DATADIR%%/gc.val
+%%DATADIR%%/humrep.fsa
+%%DATADIR%%/lineages.txt
+%%DATADIR%%/makerpt.prt
+%%DATADIR%%/ncbiendo.dat
+%%DATADIR%%/ncbipnam.dat
+%%DATADIR%%/ncbipros.dat
+%%DATADIR%%/ncbiren.dat
+%%DATADIR%%/ncbirnam.dat
+%%DATADIR%%/objprt.prt
+%%DATADIR%%/pubkey.enc
+%%DATADIR%%/seqcode.prt
+%%DATADIR%%/seqcode.val
+%%DATADIR%%/sequin.hlp
+%%DATADIR%%/sgmlbb.ent
+%%DATADIR%%/taxlist.txt
+@dirrm %%DATADIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/man
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/images
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm lib/ncbi
+@dirrm include/ncbi/connect
+@dirrm include/ncbi