- Update to 2.2.10 from 20041020

- Transfer maintainership

PR:		ports/67735
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:	old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html

6 files changed, 161 insertions, 196 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index c946237665c1..45f9e1f355c5 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -1,3 +1,4 @@
+# ex:ts=8
 # New ports collection makefile for:	NCBI
 # Date created:         03 April 2000
 # Whom:                 tonym
@@ -6,44 +7,92 @@
 #
 
 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@biolateral.com.au
+MAINTAINER=	fernan@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:
-#
+# 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
 
-DUMMYMAKE=	Makefile
-DOCDIR=		${PREFIX}/share/doc/${PORTNAME}
-CPIO=		cpio --quiet -pdum -R
+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
 
-#
-# 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.
-#
+# 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
+
+# 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
 
-pre-configure:
-	@${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
+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 --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index 282f0acf867f..a212fe682075 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -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 --git a/biology/ncbi-toolkit/files/Makefile b/biology/ncbi-toolkit/files/Makefile
deleted file mode 100644
index ee0f54493ca9..000000000000
--- a/biology/ncbi-toolkit/files/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# $FreeBSD$
-
-all:
-	cd ..; ./ncbi/make/makedis.csh
-
-install:
-	cd build; $(MAKE) install
diff --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa
deleted file mode 100644
index 65458348ad2a..000000000000
--- a/biology/ncbi-toolkit/files/patch-aa
+++ /dev/null
@@ -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 --git a/biology/ncbi-toolkit/files/patch-ncbilcl.fbd b/biology/ncbi-toolkit/files/patch-ncbilcl.fbd
deleted file mode 100644
index 75dae534e758..000000000000
--- a/biology/ncbi-toolkit/files/patch-ncbilcl.fbd
+++ /dev/null
@@ -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 --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index 08b9f8f2544d..021d9778be6c 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -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/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
@@ -121,6 +143,7 @@ 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
@@ -131,7 +154,6 @@ include/ncbi/cdconfig.h
 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/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
@@ -150,36 +173,6 @@ include/ncbi/cn3dsave.h
 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/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/id1.h
 include/ncbi/id1arch.h
 include/ncbi/id1gen.h
 include/ncbi/id1map.h
@@ -243,7 +236,6 @@ include/ncbi/jsavlt.h
 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/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
@@ -451,15 +444,16 @@ include/ncbi/suggen.h
 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/vast2mage.h
 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/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
@@ -557,16 +549,17 @@ lib/ncbi/libvibrant.a
 %%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 @@ lib/ncbi/libvibrant.a
 %%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 @@ lib/ncbi/libvibrant.a
 %%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 @@ lib/ncbi/libvibrant.a
 %%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 +724,13 @@ lib/ncbi/libvibrant.a
 %%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
+@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%%
+@dirrm %%DATADIR%%