4 files changed, 60 insertions, 44 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index e9e5946f14d4..b1d3183c1524 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2005.06.05
+PORTVERSION=	2005.12.06
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -32,12 +32,12 @@ PKGMESSAGE=	${WRKDIR}/pkg-message
 # change in the future with the addition of selectable knobs or
 # new slave ports
 
-TOOLKIT_EXE=	asn2ff asn2gb asn2xml asndhuff checksub debruijn \
-		entrcmd fa2htgs findspl getseq getfeat getmesh \
+TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \
+		debruijn entrcmd fa2htgs findspl getseq getfeat getmesh \
 		getpub gil2bin idfetch indexpub makeset tbl2asn vecscreen
 BLAST_EXE=	bl2seq blast blastall blastcl3 blastclust blastpgp copymat \
 		fastacmd formatdb impala makemat megablast rpsblast seedtop
-X11_EXE=	Nentrez Psequin ddv entrez2 netentcf udv
+X11_EXE=	Nentrez Psequin ddv entrez2 netentcf sbtedit udv
 
 # and these are the man pages we have
 MAN1=	Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \
@@ -93,7 +93,7 @@ post-install:
 .endif
 
 .if !defined(BATCH)
-	@ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${.CURDIR}/pkg-message > ${PKGMESSAGE}
+	@ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${FILESDIR}/pkg-message.in > ${PKGMESSAGE}
 	@ ${CAT} ${PKGMESSAGE}
 .endif
 
diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index d9f8d695ff8f..82242ab79d44 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -1,2 +1,3 @@
-MD5 (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 61864b4999390eb69e60734b3b02c149
-SIZE (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 14458684
+MD5 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 50a83a509b67fd8f317b0da42703de1d
+SHA256 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 0b409557d6601b8703328cd1ae997985677416e9ad9375e57b298113ecaaeeda
+SIZE (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 14693833
diff --git a/biology/ncbi-toolkit/pkg-message b/biology/ncbi-toolkit/files/pkg-message.in
index 97eed5af5f33..97eed5af5f33 100644
--- a/biology/ncbi-toolkit/pkg-message
+++ b/biology/ncbi-toolkit/files/pkg-message.in
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index f658dffb0a95..65243b4295eb 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -14,8 +14,10 @@ bin/rpsblast
 bin/seedtop
 bin/asn2ff
 bin/asn2gb
+bin/asn2idx
 bin/asn2xml
 bin/asndhuff
+bin/asntool
 bin/checksub
 bin/debruijn
 bin/entrcmd
@@ -36,6 +38,7 @@ bin/Nentrez
 bin/Psequin
 bin/entrez2
 bin/netentcf
+bin/sbtedit
 bin/udv
 include/ncbi/connect/connect_export.h
 include/ncbi/connect/ncbi_ansi_ext.h
@@ -72,11 +75,9 @@ include/ncbi/connect/ncbi_types.h
 include/ncbi/connect/ncbi_util.h
 include/ncbi/FSpCompat.h
 include/ncbi/FullPath.h
-include/ncbi/Mode_condition.h
 include/ncbi/MoreCarbonAccessors.h
 include/ncbi/MoreFilesExtras.h
 include/ncbi/MoreFilesX.h
-include/ncbi/NRdefs.h
 include/ncbi/Optimization.h
 include/ncbi/OptimizationEnd.h
 include/ncbi/PubStructAsn.h
@@ -180,6 +181,10 @@ include/ncbi/cn3dsave.h
 include/ncbi/cn3dshim.h
 include/ncbi/cn3dstyl.h
 include/ncbi/cn3dxprt.h
+include/ncbi/compo_heap.h
+include/ncbi/compo_mode_condition.h
+include/ncbi/composition_adjustment.h
+include/ncbi/composition_constants.h
 include/ncbi/corematx.h
 include/ncbi/db_list.h
 include/ncbi/ddvclick.h
@@ -257,6 +262,7 @@ include/ncbi/mapproj.h
 include/ncbi/mappubme.h
 include/ncbi/maputil.h
 include/ncbi/matrix.h
+include/ncbi/matrix_frequency_data.h
 include/ncbi/mbalign.h
 include/ncbi/mblast.h
 include/ncbi/mconsist.h
@@ -313,17 +319,13 @@ include/ncbi/netentr.h
 include/ncbi/netlib.h
 include/ncbi/netpriv.h
 include/ncbi/netscape.h
-include/ncbi/ni_asn.h
 include/ncbi/ni_defin.h
-include/ncbi/ni_encr.h
 include/ncbi/ni_error.h
 include/ncbi/ni_lib.h
 include/ncbi/ni_lib_.h
-include/ncbi/ni_list.h
-include/ncbi/ni_msg.h
 include/ncbi/ni_net.h
 include/ncbi/ni_types.h
-include/ncbi/nlm_numerics.h
+include/ncbi/nlm_linear_algebra.h
 include/ncbi/objacces.h
 include/ncbi/objalign.h
 include/ncbi/objalignloc.h
@@ -369,6 +371,7 @@ include/ncbi/objtax1.h
 include/ncbi/objtax3.h
 include/ncbi/objtseq.h
 include/ncbi/odlbox.h
+include/ncbi/optimize_target_freq.h
 include/ncbi/panels.h
 include/ncbi/parsegb.h
 include/ncbi/pcre.h
@@ -391,8 +394,8 @@ include/ncbi/prunebsc.h
 include/ncbi/pubdesc.h
 include/ncbi/puberr.h
 include/ncbi/qblastapi.h
-include/ncbi/re_newton.h
 include/ncbi/readdb.h
+include/ncbi/redo_alignment.h
 include/ncbi/regex.h
 include/ncbi/rpsutil.h
 include/ncbi/saldist.h
@@ -437,6 +440,7 @@ include/ncbi/sequtil.h
 include/ncbi/shim3d.h
 include/ncbi/simple.h
 include/ncbi/simutil.h
+include/ncbi/smith_waterman.h
 include/ncbi/spell.h
 include/ncbi/spellapi.h
 include/ncbi/spidey.h
@@ -529,6 +533,7 @@ include/ncbi/wwwblast.h
 include/ncbi/xmlblast.h
 lib/ncbi/libblast.a
 lib/ncbi/libblastapi.a
+lib/ncbi/libblastcompadj.a
 lib/ncbi/libddvlib.a
 lib/ncbi/libncbi.a
 lib/ncbi/libncbiCacc.a
@@ -574,9 +579,9 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf
+%%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/update_blastdb.pl
 %%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl
-%%PORTDOCS%%%%DOCSDIR%%/blastdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/blastftp.txt
 %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
 %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
 %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc
@@ -584,34 +589,37 @@ 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
+%%PORTDOCS%%%%DOCSDIR%%/images/cds_edit.png
+%%PORTDOCS%%%%DOCSDIR%%/images/contact.png
+%%PORTDOCS%%%%DOCSDIR%%/images/desktop.png
+%%PORTDOCS%%%%DOCSDIR%%/images/format.png
+%%PORTDOCS%%%%DOCSDIR%%/images/genbank.png
+%%PORTDOCS%%%%DOCSDIR%%/images/graphic.png
+%%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png
 %%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/blastclust.1
+%%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png
+%%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png
+%%PORTDOCS%%%%DOCSDIR%%/images/nucset.png
+%%PORTDOCS%%%%DOCSDIR%%/images/nucsing1.png
+%%PORTDOCS%%%%DOCSDIR%%/images/nucsing2.png
+%%PORTDOCS%%%%DOCSDIR%%/images/organism.png
+%%PORTDOCS%%%%DOCSDIR%%/images/props_pg.png
+%%PORTDOCS%%%%DOCSDIR%%/images/protein1.png
+%%PORTDOCS%%%%DOCSDIR%%/images/protein2.png
+%%PORTDOCS%%%%DOCSDIR%%/images/sequence.png
+%%PORTDOCS%%%%DOCSDIR%%/images/submit.png
+%%PORTDOCS%%%%DOCSDIR%%/images/update.png
+%%PORTDOCS%%%%DOCSDIR%%/images/validate.png
+%%PORTDOCS%%%%DOCSDIR%%/images/welcome.png
+%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1
 %%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1
 %%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1
 %%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1
-%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1
+
 %%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1
 %%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1
 %%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1
@@ -620,6 +628,7 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/man/blast.1
 %%PORTDOCS%%%%DOCSDIR%%/man/blastall.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
@@ -630,16 +639,15 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1
 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
 %%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1
-%%PORTDOCS%%%%DOCSDIR%%/man/udv.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/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/idfetch.1
 %%PORTDOCS%%%%DOCSDIR%%/man/impala.1
@@ -651,6 +659,7 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1
 %%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1
 %%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1
+%%PORTDOCS%%%%DOCSDIR%%/man/udv.1
 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt
 %%PORTDOCS%%%%DOCSDIR%%/sdk.doc
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
@@ -712,6 +721,12 @@ lib/ncbi/libvibrant.a
 %%DATADIR%%/KSpyr.flt
 %%DATADIR%%/PAM30
 %%DATADIR%%/PAM70
+%%DATADIR%%/UniVec.nhr
+%%DATADIR%%/UniVec.nin
+%%DATADIR%%/UniVec.nsq
+%%DATADIR%%/UniVec_Core.nhr
+%%DATADIR%%/UniVec_Core.nin
+%%DATADIR%%/UniVec_Core.nsq
 %%DATADIR%%/asn2ff.prt
 %%DATADIR%%/blast.prt
 %%DATADIR%%/bstdt.prt
@@ -744,4 +759,4 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/man
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%DATADIR%%
+@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true