ports/133099: [maintainer-update] update biology/ncbi-toolkit to latest version

Fernan Aguero fernan.aguero at gmail.com
Thu Mar 26 17:20:04 UTC 2009 

>Number:         133099
>Category:       ports
>Synopsis:       [maintainer-update] update biology/ncbi-toolkit to latest version
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Thu Mar 26 17:20:01 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        FreeBSD 6.3-RELEASE-p1 i386
>Organization:
IIB-UNSAM
>Environment:

  FreeBSD gama.iib.unsam.edu.ar 6.3-RELEASE-p1 FreeBSD 6.3-RELEASE-p1 #0:
  Wed Apr  2 18:37:14 ART 2008
  fernan at gama.iib.unsam.edu.ar:/usr/obj/freebsd/freebsd-6.3/src/sys/GAMA
  i386

	<machine, os, target, libraries (multiple lines)>
>Description:
	<precise description of the problem (multiple lines)>
	This PR updates ncbi-toolkit to the latest version. This should fix
the problem reported in PR ports/128271.

>How-To-Repeat:
	<code/input/activities to reproduce the problem (multiple lines)>
	
>Fix:

	<how to correct or work around the problem, if known (multiple lines)>



--- ncbi-toolkit.diff begins here ---
diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/Makefile
ncbi-toolkit/Makefile
--- /usr/ports/biology/ncbi-toolkit/Makefile	2008-05-07 08:41:14.000000000 -0300
+++ ncbi-toolkit/Makefile	2009-03-26 09:28:03.000000000 -0300
@@ -7,8 +7,7 @@
 #

 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2006.05.07	# containing BLAST v2.2.14
-PORTREVISION=	1
+PORTVERSION=	2009.03.01	# containing BLAST v2.2.19
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -34,23 +33,33 @@
 # new slave ports

 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 sbtedit udv
+		debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \
+		idfetch indexpub makeset tbl2asn vecscreen demo_regexp \
+		demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp
+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=	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 \
+MAN1=	asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1	asn2xml.1 \
+	asndhuff.1 asnval.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
+	copymat.1 ddv.1 debruijn.1 errhdr.1 fa2htgs.1 fastacmd.1 \
+	findspl.1 fmerge.1 formatdb.1 getmesh.1 getpub.1 gil2bin.1 \
+	idfetch.1 indexpub.1 makemat.1 makeset.1 sbtedit.1 tbl2asn.1 \
+	udv.1 vecscreen.1 Psequin.1 asn2all.1 asntool.1 entrez2.1 \
+	formatrpsdb.1
+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 seedtop.1 blast.1 rpsblast.1

 post-patch:
 	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/distinfo
ncbi-toolkit/distinfo
--- /usr/ports/biology/ncbi-toolkit/distinfo	2006-06-06 09:05:19.000000000 -0300
+++ ncbi-toolkit/distinfo	2009-03-25 20:12:58.000000000 -0300
@@ -1,3 +1,3 @@
-MD5 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 1c00462385fbf382c99ff65f34c0d09a
-SHA256 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) =
b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129
-SIZE (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 15396356
+MD5 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = af10869758e3ea11ae12f97332742629
+SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) =
631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
+SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732
diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/pkg-plist
ncbi-toolkit/pkg-plist
--- /usr/ports/biology/ncbi-toolkit/pkg-plist	2006-06-06
09:05:19.000000000 -0300
+++ ncbi-toolkit/pkg-plist	2009-03-26 09:37:01.000000000 -0300
@@ -1,5 +1,4 @@
 bin/bl2seq
-bin/blast
 bin/blastall
 bin/blastcl3
 bin/blastclust
@@ -7,11 +6,13 @@
 bin/copymat
 bin/fastacmd
 bin/formatdb
+bin/formatrpsdb
 bin/impala
 bin/makemat
 bin/megablast
 bin/rpsblast
 bin/seedtop
+bin/taxblast
 bin/asn2ff
 bin/asn2gb
 bin/asn2idx
@@ -23,8 +24,6 @@
 bin/entrcmd
 bin/fa2htgs
 bin/findspl
-bin/getseq
-bin/getfeat
 bin/getmesh
 bin/getpub
 bin/ddv
@@ -34,10 +33,16 @@
 bin/makeset
 bin/tbl2asn
 bin/vecscreen
+bin/demo_regexp
+bin/demo_regexp_grep
+bin/errhdr
+bin/gene2xml
+bin/ncbisort
+bin/seqtest
+bin/test_regexp
 bin/Nentrez
 bin/Psequin
 bin/entrez2
-bin/netentcf
 bin/sbtedit
 bin/udv
 include/ncbi/connect/connect_export.h
@@ -48,12 +53,14 @@
 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
@@ -68,11 +75,11 @@
 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_socketp.h
 include/ncbi/connect/ncbi_types.h
 include/ncbi/connect/ncbi_util.h
 include/ncbi/FSpCompat.h
@@ -90,6 +97,8 @@
 include/ncbi/accentr.h
 include/ncbi/accid1.h
 include/ncbi/accutils.h
+include/ncbi/acerdapi.h
+include/ncbi/aceread.h
 include/ncbi/actutils.h
 include/ncbi/algorend.h
 include/ncbi/alignloc.h
@@ -125,11 +134,13 @@
 include/ncbi/asnid0.h
 include/ncbi/asninsdseq.h
 include/ncbi/asnloc.h
+include/ncbi/asnmacro.h
 include/ncbi/asnmdrs.h
 include/ncbi/asnmedli.h
 include/ncbi/asnmim.h
 include/ncbi/asnmime.h
 include/ncbi/asnmla.h
+include/ncbi/asnmla2.h
 include/ncbi/asnneten.h
 include/ncbi/asnproj.h
 include/ncbi/asnprt.h
@@ -139,6 +150,7 @@
 include/ncbi/asnseq.h
 include/ncbi/asnsset.h
 include/ncbi/asnsubmt.h
+include/ncbi/asntable.h
 include/ncbi/asntax1.h
 include/ncbi/asntax3.h
 include/ncbi/asntaxon.h
@@ -147,6 +159,7 @@
 include/ncbi/binary.h
 include/ncbi/biosrc.h
 include/ncbi/blast.h
+include/ncbi/blast_dust.h
 include/ncbi/blastconcat.h
 include/ncbi/blastconcatdef.h
 include/ncbi/blastdef.h
@@ -255,6 +268,8 @@
 include/ncbi/lnfac.h
 include/ncbi/lookup.h
 include/ncbi/lsqfetch.h
+include/ncbi/macroapi.h
+include/ncbi/macrodlg.h
 include/ncbi/mapcn3d.h
 include/ncbi/mapgene.h
 include/ncbi/mapmime.h
@@ -275,6 +290,8 @@
 include/ncbi/mimapi.h
 include/ncbi/mkbioseq.h
 include/ncbi/mmdb1.h
+include/ncbi/mla2api.h
+include/ncbi/mlkludge.h
 include/ncbi/mmdb2.h
 include/ncbi/mmdb3.h
 include/ncbi/mmdbapi.h
@@ -348,12 +365,14 @@
 include/ncbi/objgen.h
 include/ncbi/objinsdseq.h
 include/ncbi/objloc.h
+include/ncbi/objmacro.h
 include/ncbi/objmdrs.h
 include/ncbi/objmedli.h
 include/ncbi/objmgr.h
 include/ncbi/objmim.h
 include/ncbi/objmime.h
 include/ncbi/objmla.h
+include/ncbi/objmla2.h
 include/ncbi/objmmdb1.h
 include/ncbi/objmmdb2.h
 include/ncbi/objmmdb3.h
@@ -369,6 +388,7 @@
 include/ncbi/objspell.h
 include/ncbi/objsset.h
 include/ncbi/objsub.h
+include/ncbi/objtable.h
 include/ncbi/objtax1.h
 include/ncbi/objtax3.h
 include/ncbi/objtseq.h
@@ -519,6 +539,7 @@
 include/ncbi/vibforms.h
 include/ncbi/vibgraph.h
 include/ncbi/vibincld.h
+include/ncbi/vibmain.h
 include/ncbi/vibmouse.h
 include/ncbi/vibpcc.h
 include/ncbi/vibprocs.h
@@ -584,7 +605,6 @@
 %%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%%/dispatcher.html
 %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
@@ -619,26 +639,30 @@
 %%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/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/entrcmd.1
 %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1
 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
 %%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1
@@ -648,20 +672,27 @@
 %%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/getfeat.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/netentcf.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
@@ -702,17 +733,26 @@
 %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css
 %%PORTDOCS%%%%DOCSDIR%%/sequin.htm
 %%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt
-%%DATADIR%%/16Score.nhr
-%%DATADIR%%/16Score.nin
-%%DATADIR%%/16Score.nsq
+%%DATADIR%%/16SCore.nhr
+%%DATADIR%%/16SCore.nin
+%%DATADIR%%/16SCore.nsq
 %%DATADIR%%/BLOSUM45
+%%DATADIR%%/BLOSUM50
 %%DATADIR%%/BLOSUM62
 %%DATADIR%%/BLOSUM80
+%%DATADIR%%/BLOSUM90
+%%DATADIR%%/Combined16SrRNA.nhr
+%%DATADIR%%/Combined16SrRNA.nin
+%%DATADIR%%/Combined16SrRNA.nsq
+%%DATADIR%%/Combined16SrRNA_2-12-2008.nhr
+%%DATADIR%%/Combined16SrRNA_2-12-2008.nin
+%%DATADIR%%/Combined16SrRNA_2-12-2008.nsq
 %%DATADIR%%/ContactPotential
 %%DATADIR%%/KSat.flt
 %%DATADIR%%/KSchoth.flt
 %%DATADIR%%/KSesigc.mat
 %%DATADIR%%/KSesigl.mat
+%%DATADIR%%/PAM250
 %%DATADIR%%/KSgc.flt
 %%DATADIR%%/KShopp.flt
 %%DATADIR%%/KSkyte.flt
@@ -725,8 +765,14 @@
 %%DATADIR%%/KSpsigl.mat
 %%DATADIR%%/KSpur.flt
 %%DATADIR%%/KSpyr.flt
+%%DATADIR%%/LSURef_93.fasta.nhr
+%%DATADIR%%/LSURef_93.fasta.nin
+%%DATADIR%%/LSURef_93.fasta.nsq
 %%DATADIR%%/PAM30
 %%DATADIR%%/PAM70
+%%DATADIR%%/SSURef_93.fasta.nhr
+%%DATADIR%%/SSURef_93.fasta.nin
+%%DATADIR%%/SSURef_93.fasta.nsq
 %%DATADIR%%/UniVec.nhr
 %%DATADIR%%/UniVec.nin
 %%DATADIR%%/UniVec.nsq
@@ -737,11 +783,17 @@
 %%DATADIR%%/blast.prt
 %%DATADIR%%/bstdt.prt
 %%DATADIR%%/bstdt.val
+%%DATADIR%%/country_lat_lon.txt
+%%DATADIR%%/ecnum_ambiguous.txt
+%%DATADIR%%/ecnum_deleted.txt
+%%DATADIR%%/ecnum_replaced.txt
+%%DATADIR%%/ecnum_specific.txt
 %%DATADIR%%/featdef.prt
 %%DATADIR%%/featdef.val
 %%DATADIR%%/gc.prt
 %%DATADIR%%/gc.val
 %%DATADIR%%/humrep.fsa
+%%DATADIR%%/institution_codes.txt
 %%DATADIR%%/lineages.txt
 %%DATADIR%%/makerpt.prt
 %%DATADIR%%/ncbiendo.dat
@@ -751,6 +803,8 @@
 %%DATADIR%%/ncbirnam.dat
 %%DATADIR%%/objprt.prt
 %%DATADIR%%/pubkey.enc
+%%DATADIR%%/rRNA_blast.nal
+%%DATADIR%%/rRNAstrand.nal
 %%DATADIR%%/seqcode.prt
 %%DATADIR%%/seqcode.val
 %%DATADIR%%/sequin.hlp
--- ncbi-toolkit.diff ends here ---

-- 
fernan

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