5 files changed, 36 insertions, 20 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index abf90f8555bc..e9e5946f14d4 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -7,8 +7,7 @@
 #
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2004.10.20
-PORTREVISION=	1
+PORTVERSION=	2005.06.05
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -28,7 +27,7 @@ PKGMESSAGE=	${WRKDIR}/pkg-message
 # are installed in each case. This Makes Sense (TM).
 # Thus, we drop a handful of programs that are useful only as tests
 # or code examples
-# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff!)
+# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff)
 # Right now the port installs all the executables below, this may
 # change in the future with the addition of selectable knobs or
 # new slave ports
@@ -41,16 +40,16 @@ BLAST_EXE=	bl2seq blast blastall blastcl3 blastclust blastpgp copymat \
 X11_EXE=	Nentrez Psequin ddv entrez2 netentcf udv
 
 # and these are the man pages we have
-MAN1=		Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \
-		asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \
-		debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
-		fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \
-		idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.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
+MAN1=	Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \
+	asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \
+	debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
+	fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \
+	idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.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
 
 # the ncbi-toolkit provides a shell script to drive the build
 # and we use it
diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index a212fe682075..d9f8d695ff8f 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -1,2 +1,2 @@
-MD5 (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 3f82bce2a3ce549f055ff989a4b825ed
-SIZE (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 13867811
+MD5 (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 61864b4999390eb69e60734b3b02c149
+SIZE (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 14458684
diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr
index 7972d3710665..8aba6be44466 100644
--- a/biology/ncbi-toolkit/pkg-descr
+++ b/biology/ncbi-toolkit/pkg-descr
@@ -17,3 +17,5 @@ From the README:
   applications.
 
 -- Tony Maher <tonym@biolateral.com.au>
+
+WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
diff --git a/biology/ncbi-toolkit/pkg-message b/biology/ncbi-toolkit/pkg-message
index d3506163b167..97eed5af5f33 100644
--- a/biology/ncbi-toolkit/pkg-message
+++ b/biology/ncbi-toolkit/pkg-message
@@ -1,6 +1,10 @@
+=====================================================================
+
 The data files are installed in "%%PREFIX%%/share/ncbi-toolkit".
 To use them you need to create a .ncbirc file in your home directory
 with the following lines:
 
 [NCBI]
 Data=%%PREFIX%%/share/ncbi-toolkit/
+
+=====================================================================
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index 021d9778be6c..f658dffb0a95 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -39,6 +39,7 @@ bin/netentcf
 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
@@ -49,6 +50,7 @@ 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_heapmgr.h
 include/ncbi/connect/ncbi_host_info.h
 include/ncbi/connect/ncbi_host_infop.h
@@ -61,16 +63,20 @@ 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_service_misc.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_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
@@ -108,6 +114,7 @@ include/ncbi/asnbibli.h
 include/ncbi/asnblock.h
 include/ncbi/asncode.h
 include/ncbi/asnent2.h
+include/ncbi/asnentgene.h
 include/ncbi/asnfdef.h
 include/ncbi/asnfeat.h
 include/ncbi/asngbseq.h
@@ -192,8 +199,8 @@ 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
+include/ncbi/egkludge.h
 include/ncbi/ent2api.h
 include/ncbi/entrez.h
 include/ncbi/entrez2.h
@@ -272,8 +279,6 @@ include/ncbi/mmdblocl.h
 include/ncbi/motif.h
 include/ncbi/ncbi.h
 include/ncbi/ncbibs.h
-include/ncbi/ncbibuf.h
-include/ncbi/ncbicli.h
 include/ncbi/ncbidraw.h
 include/ncbi/ncbienv.h
 include/ncbi/ncbierr.h
@@ -293,14 +298,12 @@ include/ncbi/ncbiprop.h
 include/ncbi/ncbisam.h
 include/ncbi/ncbisami.h
 include/ncbi/ncbisgml.h
-include/ncbi/ncbisock.h
 include/ncbi/ncbisort.h
 include/ncbi/ncbisrti.h
 include/ncbi/ncbistd.h
 include/ncbi/ncbistr.h
 include/ncbi/ncbithr.h
 include/ncbi/ncbitime.h
-include/ncbi/ncbiurl.h
 include/ncbi/ncbiwin.h
 include/ncbi/ncbiwww.h
 include/ncbi/needleman.h
@@ -320,6 +323,7 @@ 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/objacces.h
 include/ncbi/objalign.h
 include/ncbi/objalignloc.h
@@ -330,7 +334,9 @@ include/ncbi/objblst3.h
 include/ncbi/objcdd.h
 include/ncbi/objcn3d.h
 include/ncbi/objcode.h
+include/ncbi/objegkludge.h
 include/ncbi/objent2.h
+include/ncbi/objentgene.h
 include/ncbi/objentr.h
 include/ncbi/objfdef.h
 include/ncbi/objfeat.h
@@ -385,6 +391,7 @@ 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/regex.h
 include/ncbi/rpsutil.h
@@ -560,11 +567,14 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/blast/filter.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/history.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%%/blast/scoring.pdf
+%%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl
 %%PORTDOCS%%%%DOCSDIR%%/blastdb.txt
 %%PORTDOCS%%%%DOCSDIR%%/blastftp.txt
 %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
@@ -573,6 +583,7 @@ lib/ncbi/libvibrant.a
 %%PORTDOCS%%%%DOCSDIR%%/firedialog.gif
 %%PORTDOCS%%%%DOCSDIR%%/firewall.html
 %%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh
+%%PORTDOCS%%%%DOCSDIR%%/gene2xml.txt
 %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
 %%PORTDOCS%%%%DOCSDIR%%/images/seqn01.png
 %%PORTDOCS%%%%DOCSDIR%%/images/seqn02.png