ports/67735: biology/ncbi-toolkit does not build bl2seq
Fernan Aguero
fernan at iib.unsam.edu.ar
Thu Mar 17 21:40:11 UTC 2005
The following reply was made to PR ports/67735; it has been noted by GNATS.
From: Fernan Aguero <fernan at iib.unsam.edu.ar>
To: Volker Stolz <vs at FreeBSD.org>
Cc: FreeBSD GNATS PR Submission <freebsd-gnats-submit at FreeBSD.org>
Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq
Date: Thu, 17 Mar 2005 18:37:19 -0300
--PEIAKu/WMn1b1Hv9
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
+----[ Volker Stolz <vs at FreeBSD.org> (25.Jun.2004 16:43):
|
| Synopsis: biology/ncbi-toolkit does not build bl2seq
|
+----]
Grrr, I forgot to add the patch. Here it is,
Fernan
--PEIAKu/WMn1b1Hv9
Content-Type: text/plain; charset=us-ascii
Content-Disposition: attachment; filename="ncbi-toolkit.diff"
diff -ruN /usr/ports/biology/ncbi-toolkit/Makefile ncbi-toolkit/Makefile
--- /usr/ports/biology/ncbi-toolkit/Makefile Mon Nov 8 13:04:37 2004
+++ ncbi-toolkit/Makefile Thu Mar 17 17:55:59 2005
@@ -1,3 +1,4 @@
+# ex:ts=8
# New ports collection makefile for: NCBI
# Date created: 03 April 2000
# Whom: tonym
@@ -6,44 +7,96 @@
#
PORTNAME= ncbi-toolkit
-PORTVERSION= 2004.06.16
+PORTVERSION= 2004.10.20
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME= ncbi
+DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
-MAINTAINER= tonym at biolateral.com.au
+MAINTAINER= fernan at iib.unsam.edu.ar
COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
USE_MOTIF= yes
+CPIO_ARGS= --quiet -pdum -R
+PKGMESSAGE= ${WRKDIR}/pkg-message
+# These are the executables we install.
#
-# In the files directory we have:
-#
-
-DUMMYMAKE= Makefile
-DOCDIR= ${PREFIX}/share/doc/${PORTNAME}
-CPIO= cpio --quiet -pdum -R
-
-#
-# Thus ends the definitions.
-#
-# Now we need a dummy top level Makefile as NCBI has scripts that need to
-# run from point above ncbi hierachy.
-#
-
-pre-configure:
- @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
+# We follow Debian in the separation of the port in three
+# main categories and in the selection of programs that
+# 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!)
+# 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
+
+TOOLKIT_EXE= asn2ff asn2gb asn2xml asndhuff 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
+
+# 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 bl2seq.1 blast.1 blastall.1 blastcl3.1 blastclust.1 \
+ blastpgp.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 impala.1 \
+ indexpub.1 makemat.1 makeset.1 megablast.1 netentcf.1 rpsblast.1 \
+ seedtop.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 megablast.1 blast.1 seedtop.1
+
+# the ncbi-toolkit provides a shell script to drive the build
+# and we use it
+
+do-build:
+ cd ${WRKDIR}; ./${DISTNAME}/make/makedis.csh
+
+# the ncbi-toolkit does not provide an install target
+# we thus roll our own
+
+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_PROGRAM} *.a ${PREFIX}/lib/${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)
+
+.for man in ${MAN1}
+ (cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)
+.endfor
post-install:
- ${MKDIR} ${DATADIR}
- @for file in ${WRKSRC}/data/*; do \
- ${INSTALL_DATA} $$file ${DATADIR}; \
- done
+ @${MKDIR} ${DATADIR}
+ (cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})
+
.if !defined(NOPORTDOCS)
- ${MKDIR} ${DOCDIR}
- cd ${WRKSRC}/doc && ${FIND} * | \
- ${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR}
+ @${MKDIR} ${DOCSDIR}
+ (cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
+.endif
+
+.if !defined(BATCH)
+ @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${.CURDIR}/pkg-message > ${PKGMESSAGE}
+ @ ${CAT} ${PKGMESSAGE}
.endif
- @${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE}
.include <bsd.port.mk>
diff -ruN /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo
--- /usr/ports/biology/ncbi-toolkit/distinfo Mon Nov 8 13:04:37 2004
+++ ncbi-toolkit/distinfo Mon Jan 17 12:17:05 2005
@@ -1,2 +1,2 @@
-MD5 (ncbi.tar.gz) = 12320f853acb397a14729fb0da0b09df
-SIZE (ncbi.tar.gz) = 13680457
+MD5 (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 3f82bce2a3ce549f055ff989a4b825ed
+SIZE (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 13867811
diff -ruN /usr/ports/biology/ncbi-toolkit/files/Makefile ncbi-toolkit/files/Makefile
--- /usr/ports/biology/ncbi-toolkit/files/Makefile Sun Oct 29 10:56:24 2000
+++ ncbi-toolkit/files/Makefile Wed Dec 31 21:00:00 1969
@@ -1,8 +0,0 @@
-#
-# $FreeBSD: ports/biology/ncbi-toolkit/files/Makefile,v 1.1 2000/10/29 13:56:24 jeh Exp $
-
-all:
- cd ..; ./ncbi/make/makedis.csh
-
-install:
- cd build; $(MAKE) install
diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-aa ncbi-toolkit/files/patch-aa
--- /usr/ports/biology/ncbi-toolkit/files/patch-aa Mon Nov 8 13:04:37 2004
+++ ncbi-toolkit/files/patch-aa Wed Dec 31 21:00:00 1969
@@ -1,51 +0,0 @@
---- 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
-+
-+EXE= Nentrez Psequin \
-+ asn2ff asn2gb asn2xml asndhuff asntool \
-+ blastall blastcl3 blastclust blastpgp \
-+ cdscan checksub copymat \
-+ ddv demo_regexp demo_regexp_grep dosimple \
-+ entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb \
-+ getfeat getmesh getpub getseq gil2bin \
-+ idfetch impala indexpub \
-+ makemat makeset megablast \
-+ ncbisort netentcf \
-+ rpsblast \
-+ seedtop seqtest \
-+ tbl2asn testcore testobj testval \
-+ udv vecscreen
-+
-+
-+MKDIR= /bin/mkdir -p
-+INSTALL_PROGRAM= /usr/bin/install -c
-+
-+binstall: $(EXE)
-+ ${MKDIR} ${PREFIX}/bin
-+.for f in $(EXE)
-+ ${INSTALL_PROGRAM} -s $(f) ${PREFIX}/bin
-+.endfor
-+
-+linstall: $(LIB)
-+ ${MKDIR} ${PREFIX}/lib/ncbi
-+ for file in *.a; do \
-+ ${INSTALL_PROGRAM} $$file ${PREFIX}/lib/ncbi; \
-+ done
-+
-+iinstall::
-+ ${MKDIR} ${PREFIX}/include/ncbi/connect
-+ cd ../include; \
-+ for file in *.h; do \
-+ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi; \
-+ done
-+ cd ../include/connect; \
-+ for file in *.h; do \
-+ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi/connect; \
-+ done
-+
-+install: iinstall linstall binstall
-+
diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-bl2seq ncbi-toolkit/files/patch-bl2seq
--- /usr/ports/biology/ncbi-toolkit/files/patch-bl2seq Tue Jun 8 17:23:06 2004
+++ ncbi-toolkit/files/patch-bl2seq Wed Dec 31 21:00:00 1969
@@ -1,12 +0,0 @@
---- build/makefile.orig Tue Jun 8 17:21:49 2004
-+++ build/makefile Tue Jun 8 17:22:17 2004
-@@ -899,7 +899,8 @@
- rpsblast \
- seedtop seqtest \
- tbl2asn testcore testobj testval \
-- udv vecscreen
-+ udv vecscreen \
-+ bl2seq
-
-
- MKDIR= /bin/mkdir -p
diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-ncbilcl.fbd ncbi-toolkit/files/patch-ncbilcl.fbd
--- /usr/ports/biology/ncbi-toolkit/files/patch-ncbilcl.fbd Mon May 5 09:24:08 2003
+++ ncbi-toolkit/files/patch-ncbilcl.fbd Wed Dec 31 21:00:00 1969
@@ -1,18 +0,0 @@
---- corelib/ncbilcl.fbd.orig Sat Nov 23 07:05:04 2002
-+++ corelib/ncbilcl.fbd Sat May 3 10:06:18 2003
-@@ -67,6 +67,7 @@
- /*----------------------------------------------------------------------*/
- #define SYSV_IPC_AVAIL /* System V Interprocess Communication available */
- #define _POSIX_C_SOURCE 199309L
-+#define _XOPEN_SOURCE 600 /* req. for 5.0 */
- #define HAVE_STRCASECMP 1
- #define HAVE_STRDUP 1
-
-@@ -87,6 +88,7 @@
- #include <errno.h>
- #include <float.h>
- #include <unistd.h>
-+#include <sys/select.h> /* req. for 5.0. fd_set def. moved from types.h */
-
- /* Check if there are POSIX threads available */
- #ifdef _POSIX_THREADS
diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist ncbi-toolkit/pkg-plist
--- /usr/ports/biology/ncbi-toolkit/pkg-plist Mon Nov 8 13:04:38 2004
+++ ncbi-toolkit/pkg-plist Thu Mar 17 17:54:31 2005
@@ -1,50 +1,71 @@
-bin/Nentrez
-bin/Psequin
-bin/asn2ff
-bin/asn2gb
-bin/asn2xml
-bin/asndhuff
-bin/asntool
+bin/bl2seq
+bin/blast
bin/blastall
bin/blastcl3
bin/blastclust
bin/blastpgp
-bin/cdscan
-bin/checksub
bin/copymat
-bin/ddv
-bin/demo_regexp
-bin/demo_regexp_grep
-bin/dosimple
+bin/fastacmd
+bin/formatdb
+bin/impala
+bin/makemat
+bin/megablast
+bin/rpsblast
+bin/seedtop
+bin/asn2ff
+bin/asn2gb
+bin/asn2xml
+bin/asndhuff
+bin/checksub
+bin/debruijn
bin/entrcmd
-bin/entrez2
-bin/errhdr
bin/fa2htgs
-bin/fastacmd
bin/findspl
-bin/formatdb
+bin/getseq
bin/getfeat
bin/getmesh
bin/getpub
-bin/getseq
+bin/ddv
bin/gil2bin
bin/idfetch
-bin/impala
bin/indexpub
-bin/makemat
bin/makeset
-bin/megablast
-bin/ncbisort
-bin/netentcf
-bin/rpsblast
-bin/seedtop
-bin/seqtest
bin/tbl2asn
-bin/testcore
-bin/testobj
-bin/testval
-bin/udv
bin/vecscreen
+bin/Nentrez
+bin/Psequin
+bin/entrez2
+bin/netentcf
+bin/udv
+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
@@ -109,6 +130,7 @@
include/ncbi/asnsset.h
include/ncbi/asnsubmt.h
include/ncbi/asntax1.h
+include/ncbi/asntax3.h
include/ncbi/asntaxon.h
include/ncbi/asntseq.h
include/ncbi/bandalgn.h
@@ -121,6 +143,7 @@
include/ncbi/blastkar.h
include/ncbi/blastpat.h
include/ncbi/blastpri.h
+include/ncbi/blfmtutl.h
include/ncbi/blocks.h
include/ncbi/blstspc.h
include/ncbi/blstxml.h
@@ -131,7 +154,6 @@
include/ncbi/cdd.h
include/ncbi/cddapi.h
include/ncbi/cddposutil.h
-include/ncbi/cddsrv.h
include/ncbi/cddutil.h
include/ncbi/cdentrez.h
include/ncbi/cdnewlib.h
@@ -140,6 +162,7 @@
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
@@ -150,36 +173,6 @@
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
@@ -220,12 +213,12 @@
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
@@ -243,7 +236,6 @@
include/ncbi/jzcoll.h
include/ncbi/jzmisc.h
include/ncbi/layout.h
-include/ncbi/lbapi.h
include/ncbi/legend.h
include/ncbi/list.h
include/ncbi/lnfac.h
@@ -368,6 +360,7 @@
include/ncbi/objsset.h
include/ncbi/objsub.h
include/ncbi/objtax1.h
+include/ncbi/objtax3.h
include/ncbi/objtseq.h
include/ncbi/odlbox.h
include/ncbi/panels.h
@@ -451,15 +444,16 @@
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
include/ncbi/taxblast.h
include/ncbi/taxext.h
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
@@ -502,6 +496,7 @@
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
@@ -520,12 +515,9 @@
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
lib/ncbi/libblast.a
@@ -557,16 +549,17 @@
%%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
-%%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
%%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html
%%PORTDOCS%%%%DOCSDIR%%/blast/filter.html
%%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html
+%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html
%%PORTDOCS%%%%DOCSDIR%%/blast/impala.html
%%PORTDOCS%%%%DOCSDIR%%/blast/index.html
%%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html
@@ -603,27 +596,32 @@
%%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/blastclust.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
+%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1
+%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1
+%%PORTDOCS%%%%DOCSDIR%%/man/blast.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/checksub.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/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
@@ -632,42 +630,37 @@
%%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/Makefile
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css
%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.xml
%%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF
%%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css
%%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/sniff.js
%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.xml
%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.css
%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.html
@@ -678,11 +671,11 @@
%%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/sequin-icon-win.gif
%%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-ie3.css
%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css
%%PORTDOCS%%%%DOCSDIR%%/sequin.htm
%%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt
@@ -731,13 +724,14 @@
%%DATADIR%%/sequin.hlp
%%DATADIR%%/sgmlbb.ent
%%DATADIR%%/taxlist.txt
- at 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%%
- at dirrm lib/ncbi
@dirrm include/ncbi/connect
@dirrm include/ncbi
+ at dirrm include
+ at dirrm lib/ncbi
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/man
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+ at dirrm %%DATADIR%%
diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist.bak ncbi-toolkit/pkg-plist.bak
--- /usr/ports/biology/ncbi-toolkit/pkg-plist.bak Wed Dec 31 21:00:00 1969
+++ ncbi-toolkit/pkg-plist.bak Thu Mar 17 17:52:19 2005
@@ -0,0 +1,786 @@
+bin/bl2seq
+bin/blast
+bin/blastall
+bin/blastcl3
+bin/blastclust
+bin/blastpgp
+bin/copymat
+bin/fastacmd
+bin/formatdb
+bin/impala
+bin/makemat
+bin/megablast
+bin/rpsblast
+bin/seedtop
+bin/asn2ff
+bin/asn2gb
+bin/asn2xml
+bin/asndhuff
+bin/checksub
+bin/debruijn
+bin/entrcmd
+bin/fa2htgs
+bin/findspl
+bin/getseq
+bin/getfeat
+bin/getmesh
+bin/getpub
+bin/ddv
+bin/gil2bin
+bin/idfetch
+bin/indexpub
+bin/makeset
+bin/tbl2asn
+bin/vecscreen
+bin/Nentrez
+bin/Psequin
+bin/entrez2
+bin/netentcf
+bin/udv
+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
+include/ncbi/MoreFilesExtras.h
+include/ncbi/MoreFilesX.h
+include/ncbi/Optimization.h
+include/ncbi/OptimizationEnd.h
+include/ncbi/PubStructAsn.h
+include/ncbi/a2ferr.h
+include/ncbi/a2ferrdf.h
+include/ncbi/a2fstruc.h
+include/ncbi/aacomp.h
+include/ncbi/accentr.h
+include/ncbi/accid1.h
+include/ncbi/accutils.h
+include/ncbi/actutils.h
+include/ncbi/algorend.h
+include/ncbi/alignloc.h
+include/ncbi/alignmgr.h
+include/ncbi/alignmgr2.h
+include/ncbi/alignval.h
+include/ncbi/aliparse.h
+include/ncbi/aliread.h
+include/ncbi/all.h
+include/ncbi/allpub.h
+include/ncbi/apparam.h
+include/ncbi/asn.h
+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/asnalign.h
+include/ncbi/asnbibli.h
+include/ncbi/asnblock.h
+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
+include/ncbi/asnmim.h
+include/ncbi/asnmime.h
+include/ncbi/asnmla.h
+include/ncbi/asnneten.h
+include/ncbi/asnproj.h
+include/ncbi/asnprt.h
+include/ncbi/asnpub.h
+include/ncbi/asnpubme.h
+include/ncbi/asnres.h
+include/ncbi/asnseq.h
+include/ncbi/asnsset.h
+include/ncbi/asnsubmt.h
+include/ncbi/asntax1.h
+include/ncbi/asntax3.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
+include/ncbi/blastpri.h
+include/ncbi/blfmtutl.h
+include/ncbi/blocks.h
+include/ncbi/blstspc.h
+include/ncbi/blstxml.h
+include/ncbi/bspview.h
+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/cddutil.h
+include/ncbi/cdentrez.h
+include/ncbi/cdnewlib.h
+include/ncbi/cdrgn.h
+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
+include/ncbi/cn3dmsel.h
+include/ncbi/cn3dmsg.h
+include/ncbi/cn3dopen.h
+include/ncbi/cn3dsave.h
+include/ncbi/cn3dshim.h
+include/ncbi/cn3dstyl.h
+include/ncbi/cn3dxprt.h
+include/ncbi/corematx.h
+include/ncbi/db_list.h
+include/ncbi/ddvclick.h
+include/ncbi/ddvcolor.h
+include/ncbi/ddvcreate.h
+include/ncbi/ddvgraph.h
+include/ncbi/ddvmain.h
+include/ncbi/ddvopen.h
+include/ncbi/ddvpanel.h
+include/ncbi/diagnost.h
+include/ncbi/dlogutil.h
+include/ncbi/document.h
+include/ncbi/dotmatrx.h
+include/ncbi/dotseq.h
+include/ncbi/dotviewer.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
+include/ncbi/ent2api.h
+include/ncbi/entrez.h
+include/ncbi/entrez2.h
+include/ncbi/errdefn.h
+include/ncbi/explore.h
+include/ncbi/fastadl.h
+include/ncbi/fdlKludge.h
+include/ncbi/fdlobj.h
+include/ncbi/fea2seg.h
+include/ncbi/ffprint.h
+include/ncbi/findrepl.h
+include/ncbi/fstyle.h
+include/ncbi/fstylep.h
+include/ncbi/ftusrstr.h
+include/ncbi/gapxdrop.h
+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/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
+include/ncbi/ingenext.h
+include/ncbi/ingengraph.h
+include/ncbi/ingenwin.h
+include/ncbi/jsavlt.h
+include/ncbi/jzcoll.h
+include/ncbi/jzmisc.h
+include/ncbi/layout.h
+include/ncbi/legend.h
+include/ncbi/list.h
+include/ncbi/lnfac.h
+include/ncbi/lookup.h
+include/ncbi/lsqfetch.h
+include/ncbi/mapcn3d.h
+include/ncbi/mapgene.h
+include/ncbi/mapmime.h
+include/ncbi/mapmla.h
+include/ncbi/mappingp.h
+include/ncbi/mapproj.h
+include/ncbi/mappubme.h
+include/ncbi/maputil.h
+include/ncbi/matrix.h
+include/ncbi/mbalign.h
+include/ncbi/mblast.h
+include/ncbi/mconsist.h
+include/ncbi/mdrcherr.h
+include/ncbi/medarch.h
+include/ncbi/medutil.h
+include/ncbi/medview.h
+include/ncbi/mimapi.h
+include/ncbi/mkbioseq.h
+include/ncbi/mmdb1.h
+include/ncbi/mmdb2.h
+include/ncbi/mmdb3.h
+include/ncbi/mmdbapi.h
+include/ncbi/mmdbapi1.h
+include/ncbi/mmdbapi2.h
+include/ncbi/mmdbapi3.h
+include/ncbi/mmdbapi4.h
+include/ncbi/mmdbdata.h
+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
+include/ncbi/ncbifile.h
+include/ncbi/ncbigif.h
+include/ncbi/ncbilang.h
+include/ncbi/ncbilcl.h
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+include/ncbi/ncbinet.h
+include/ncbi/ncbiopt.h
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+include/ncbi/ncbiurl.h
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+include/ncbi/ncbiwww.h
+include/ncbi/needleman.h
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+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/objacces.h
+include/ncbi/objalign.h
+include/ncbi/objalignloc.h
+include/ncbi/objall.h
+include/ncbi/objbibli.h
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+include/ncbi/objblst3.h
+include/ncbi/objcdd.h
+include/ncbi/objcn3d.h
+include/ncbi/objcode.h
+include/ncbi/objent2.h
+include/ncbi/objentr.h
+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
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+include/ncbi/objmim.h
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+include/ncbi/objmla.h
+include/ncbi/objmmdb1.h
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+include/ncbi/objneten.h
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+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
+include/ncbi/objtax3.h
+include/ncbi/objtseq.h
+include/ncbi/odlbox.h
+include/ncbi/panels.h
+include/ncbi/parsegb.h
+include/ncbi/pcre.h
+include/ncbi/pcre_config.h
+include/ncbi/pcre_internal.h
+include/ncbi/pcreposix.h
+include/ncbi/pdiagnos.h
+include/ncbi/pgppop.h
+include/ncbi/pictur3d.h
+include/ncbi/picture.h
+include/ncbi/picturep.h
+include/ncbi/pmfapi.h
+include/ncbi/pobutil.h
+include/ncbi/posit.h
+include/ncbi/ppict3d.h
+include/ncbi/profiles.h
+include/ncbi/prtgene.h
+include/ncbi/prtutil.h
+include/ncbi/prunebsc.h
+include/ncbi/pubdesc.h
+include/ncbi/puberr.h
+include/ncbi/qblastapi.h
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+include/ncbi/rpsutil.h
+include/ncbi/saldist.h
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+include/ncbi/salign.h
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+include/ncbi/satutil.h
+include/ncbi/scoremat.h
+include/ncbi/sdisplay.h
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+include/ncbi/seqanal.h
+include/ncbi/seqcons.h
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+include/ncbi/seqsplit.h
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+include/ncbi/simutil.h
+include/ncbi/spell.h
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+ at dirrm include/ncbi/connect
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+ at dirrm lib
+ at dirrm share/doc/ncbi-toolkit/blast
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diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist.orig ncbi-toolkit/pkg-plist.orig
--- /usr/ports/biology/ncbi-toolkit/pkg-plist.orig Wed Dec 31 21:00:00 1969
+++ ncbi-toolkit/pkg-plist.orig Mon Jan 17 13:51:23 2005
@@ -0,0 +1,743 @@
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+bin/asntool
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+bin/blastclust
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+bin/checksub
+bin/copymat
+bin/ddv
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+bin/demo_regexp_grep
+bin/dosimple
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+bin/entrez2
+bin/errhdr
+bin/fa2htgs
+bin/fastacmd
+bin/findspl
+bin/formatdb
+bin/getfeat
+bin/getmesh
+bin/getpub
+bin/getseq
+bin/gil2bin
+bin/idfetch
+bin/impala
+bin/indexpub
+bin/makemat
+bin/makeset
+bin/megablast
+bin/ncbisort
+bin/netentcf
+bin/rpsblast
+bin/seedtop
+bin/seqtest
+bin/tbl2asn
+bin/testcore
+bin/testobj
+bin/testval
+bin/udv
+bin/vecscreen
+include/ncbi/FSpCompat.h
+include/ncbi/FullPath.h
+include/ncbi/MoreCarbonAccessors.h
+include/ncbi/MoreFilesExtras.h
+include/ncbi/MoreFilesX.h
+include/ncbi/Optimization.h
+include/ncbi/OptimizationEnd.h
+include/ncbi/PubStructAsn.h
+include/ncbi/a2ferr.h
+include/ncbi/a2ferrdf.h
+include/ncbi/a2fstruc.h
+include/ncbi/aacomp.h
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+include/ncbi/objseq.h
+include/ncbi/objspell.h
+include/ncbi/objsset.h
+include/ncbi/objsub.h
+include/ncbi/objtax1.h
+include/ncbi/objtseq.h
+include/ncbi/odlbox.h
+include/ncbi/panels.h
+include/ncbi/parsegb.h
+include/ncbi/pcre.h
+include/ncbi/pcre_config.h
+include/ncbi/pcre_internal.h
+include/ncbi/pcreposix.h
+include/ncbi/pdiagnos.h
+include/ncbi/pgppop.h
+include/ncbi/pictur3d.h
+include/ncbi/picture.h
+include/ncbi/picturep.h
+include/ncbi/pmfapi.h
+include/ncbi/pobutil.h
+include/ncbi/posit.h
+include/ncbi/ppict3d.h
+include/ncbi/profiles.h
+include/ncbi/prtgene.h
+include/ncbi/prtutil.h
+include/ncbi/prunebsc.h
+include/ncbi/pubdesc.h
+include/ncbi/puberr.h
+include/ncbi/qblastapi.h
+include/ncbi/readdb.h
+include/ncbi/regex.h
+include/ncbi/rpsutil.h
+include/ncbi/saldist.h
+include/ncbi/saled.h
+include/ncbi/saledit.h
+include/ncbi/salfiles.h
+include/ncbi/salign.h
+include/ncbi/salmedia.h
+include/ncbi/salogif.h
+include/ncbi/salpacc.h
+include/ncbi/salpanel.h
+include/ncbi/salparam.h
+include/ncbi/salpedit.h
+include/ncbi/salprop.h
+include/ncbi/salpstat.h
+include/ncbi/salptool.h
+include/ncbi/salsa.h
+include/ncbi/salsap.h
+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
+include/ncbi/seg.h
+include/ncbi/seqanal.h
+include/ncbi/seqcons.h
+include/ncbi/seqfltr.h
+include/ncbi/seqgraph.h
+include/ncbi/seqgrphx.h
+include/ncbi/seqmgr.h
+include/ncbi/seqmtrx.h
+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
+include/ncbi/strimprt.h
+include/ncbi/strucapi.h
+include/ncbi/stsutil.h
+include/ncbi/subutil.h
+include/ncbi/suggapi.h
+include/ncbi/suggen.h
+include/ncbi/suggest.h
+include/ncbi/suggslp.h
+include/ncbi/sugmap.h
+include/ncbi/sugprefx.h
+include/ncbi/tax1map.h
+include/ncbi/taxblast.h
+include/ncbi/taxext.h
+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
+include/ncbi/toasn3.h
+include/ncbi/tofasta.h
+include/ncbi/tofile.h
+include/ncbi/tomedlin.h
+include/ncbi/toporg.h
+include/ncbi/tree.h
+include/ncbi/treemgr.h
+include/ncbi/treeview.h
+include/ncbi/treevint.h
+include/ncbi/tsprintf.h
+include/ncbi/txalign.h
+include/ncbi/txclient.h
+include/ncbi/txcommon.h
+include/ncbi/udvdef.h
+include/ncbi/udviewer.h
+include/ncbi/udvseq.h
+include/ncbi/undefwin.h
+include/ncbi/urkbias.h
+include/ncbi/urkcnsrt.h
+include/ncbi/urkdust.h
+include/ncbi/urkepi.h
+include/ncbi/urkfltr.h
+include/ncbi/urkgraph.h
+include/ncbi/urkpcc.h
+include/ncbi/urkptpf.h
+include/ncbi/urksigu.h
+include/ncbi/urktree.h
+include/ncbi/urkutil.h
+include/ncbi/urlquery.h
+include/ncbi/utilpars.h
+include/ncbi/utilpub.h
+include/ncbi/valid.h
+include/ncbi/validatr.h
+include/ncbi/validerr.h
+include/ncbi/vast2cn3d.h
+include/ncbi/vast2mage.h
+include/ncbi/vast2pdb.h
+include/ncbi/vastlocl.h
+include/ncbi/vastsrv.h
+include/ncbi/vecscnapi.h
+include/ncbi/vecscrn.h
+include/ncbi/vibdefns.h
+include/ncbi/vibfltr.h
+include/ncbi/vibforms.h
+include/ncbi/vibgraph.h
+include/ncbi/vibincld.h
+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
+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
+%%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css
+%%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
+ at 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%%
+ at dirrm lib/ncbi
+ at dirrm include/ncbi/connect
+ at dirrm include/ncbi
--PEIAKu/WMn1b1Hv9--
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