Attachment #132280 for bug #176544




# $FreeBSD: head/biology/ncbi-toolkit/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $

PORTNAME=	ncbi-toolkit
PORTVERSION=	2012.06.20	# containing BLAST v2.2.27
PORTREVISION=	1
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME=	ncbi
DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}

MAINTAINER=	ports@FreeBSD.org
COMMENT=	NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

OPTIONS_DEFINE=	DOCS

USE_MOTIF=	yes
MAKE_JOBS_UNSAFE=	yes

SUB_FILES=	pkg-message

# These are the executables we install.

# change in the future with the addition of selectable knobs or
# new slave ports

TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
		checksub debruijn demo_regexp demo_regexp_grep dosimple \
		entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
		gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
		vecscreen
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=		Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
		asntool.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 formatdb.1 formatrpsdb.1 getmesh.1 \
		getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
		taxblast.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 rpsblast.1 

.include <bsd.port.options.mk>

post-patch:
	@${REINPLACE_CMD} -e \
		's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
	@${REINPLACE_CMD} -e \
		'/^NCBI_CC/s|=.*|= ${CC}| ; \
		 /^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
		 /^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
		 s|-I/usr/X11R6/include||g ; \
		 s|-L/usr/X11R6/lib||g ; \
		 s|/usr/local|${LOCALBASE}|g ; \
		 s|-Wl,-Bstatic|| ; \
		 s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk

# the ncbi-toolkit provides a shell script to drive the build
# and we use it

.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_DATA} *.a ${PREFIX}/lib/${DISTNAME})
	@${MKDIR} ${PREFIX}/include/${DISTNAME}
	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
		${PREFIX}/include/${DISTNAME})
	@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
		${PREFIX}/include/${DISTNAME}/connect)

.for man in ${MAN1}
	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1)
.endfor

post-install:
	@${MKDIR} ${DATADIR}
	(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR})
.if ${PORT_OPTIONS:MDOCS}
.if !defined(NOPORTDOCS)
	@${MKDIR} ${DOCSDIR}
	@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
		(cd ${DOCSDIR} && ${TAR} --unlink -xf -)
	@${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
	@${FIND} ${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
	@${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
.endif
	@${CAT} ${PKGMESSAGE}

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)biology/ncbi-toolkit/distinfo (-2 / +2 lines)
1	SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df	1	SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
2	SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732	2	SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744

Line 0 Link Here

(-)biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c (+11 lines)
	1	--- corelib/ncbimisc.c.orig
	2	+++ corelib/ncbimisc.c
	3	@@ -1266,7 +1266,7 @@
	4	if (len < 1) return NULL;
	5
	6	rsult = (Nlm_CharPtr) MemNew (len + 3);
	7	- if (rsult == NULL) return;
	8	+ if (rsult == NULL) return NULL;
	9	tmp = rsult;
	10
	11	for (i = 0; /* local [i] != NULL */ i < numitems; i++) {




 SEQUIN_OPTS =
 LIBCOPY = cp -p
 SRCCOPY = ./ln-if-absent
@@ -934,17 +935,17 @@
 	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
 	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
 	$(LIBCOMPADJ) $(LIB2) $(LIB1) \

 
 udv    : $(OBJUDV)
 	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
 	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
 	$(LIB23) $(LIBCOMPADJ) $(LIB2) \
-	$(LIB1) $(VIBLIBS) $(OTHERLIBS)
+	$(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
 
 Nentrez : entrez.c $(ULIB31)
 	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
-	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
 
 # left this in (Tentrez) for script backwards compatibility
 Tentrez : entrez.c $(ULIB31)
@@ -1140,7 +1141,7 @@
 entrez2 :	entrez2.c
 	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
 		$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \

 	$(VIB_POST_LINK) entrez2
 
 # demo program (spidey)
@@ -1421,7 +1422,7 @@
 	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
 	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
 	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \

 	$(VIB_POST_LINK) Psequin
 
 # 'sbtedit' Submission Template Editor
@@ -1433,7 +1434,7 @@
 	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
 	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
 	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \

+	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
 	$(VIB_POST_LINK) sbtedit
 
 # 'streamer' Sequinesque Stream Editor

Lines 16-19 Link Here

(-)biology/ncbi-toolkit/pkg-descr (-1 / +1 lines)
16	have found it a useful and stable basis for a number of tools and	16	have found it a useful and stable basis for a number of tools and
17	applications.	17	applications.
18		18
19	WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml	19	WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html




bin/Nentrez
bin/Psequin
bin/blastcl3
bin/blastclust
bin/blastpgp
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
bin/asn2xml
bin/asndhuff
bin/asntool
bin/bl2seq
bin/blastall
bin/blastcl3
bin/blastclust
bin/blastpgp
bin/cdscan
bin/checksub
bin/copymat
bin/ddv
bin/debruijn
bin/demo_regexp
bin/demo_regexp_grep
bin/dosimple
bin/entrcmd
bin/entrez2
bin/errhdr
bin/fa2htgs
bin/fastacmd
bin/findspl
bin/formatdb
bin/formatrpsdb
bin/gene2xml
bin/getmesh
bin/getpub
bin/ddv
bin/gil2bin
bin/idfetch
bin/impala
bin/indexpub
bin/makemat
bin/makeset
bin/megablast
bin/vecscreen
bin/demo_regexp
bin/demo_regexp_grep
bin/errhdr
bin/gene2xml
bin/ncbisort
bin/rpsblast
bin/test_regexp
bin/Nentrez
bin/Psequin
bin/entrez2
bin/sbtedit
bin/seedtop
bin/seqtest
bin/taxblast
bin/tbl2asn
bin/udv
bin/vecscreen
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
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
include/ncbi/connect/ncbi_http_connector.h
include/ncbi/connect/ncbi_lb.h
include/ncbi/connect/ncbi_lbsmd.h
include/ncbi/connect/ncbi_local.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_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
include/ncbi/FullPath.h
include/ncbi/MoreCarbonAccessors.h

include/ncbi/asntax3.h
include/ncbi/asntaxon.h
include/ncbi/asntseq.h
include/ncbi/asnvalid.h
include/ncbi/bandalgn.h
include/ncbi/binary.h
include/ncbi/biosrc.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/cn3dshim.h
include/ncbi/cn3dstyl.h
include/ncbi/cn3dxprt.h
include/ncbi/codon.h
include/ncbi/compo_heap.h
include/ncbi/compo_mode_condition.h
include/ncbi/composition_adjustment.h
include/ncbi/composition_constants.h
include/ncbi/connect/connect_export.h
include/ncbi/connect/ncbi_ansi_ext.h
include/ncbi/connect/ncbi_assert.h
include/ncbi/connect/ncbi_base64.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_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
include/ncbi/connect/ncbi_http_connector.h
include/ncbi/connect/ncbi_lb.h
include/ncbi/connect/ncbi_lbsmd.h
include/ncbi/connect/ncbi_local.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_socket_unix.h
include/ncbi/connect/ncbi_socketp.h
include/ncbi/connect/ncbi_types.h
include/ncbi/connect/ncbi_util.h
include/ncbi/connect/ncbi_version.h
include/ncbi/corematx.h
include/ncbi/db_list.h
include/ncbi/ddvclick.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

include/ncbi/medview.h
include/ncbi/mimapi.h
include/ncbi/mkbioseq.h
include/ncbi/mmdb1.h
include/ncbi/mla2api.h
include/ncbi/mlkludge.h
include/ncbi/mmdb1.h
include/ncbi/mmdb2.h
include/ncbi/mmdb3.h
include/ncbi/mmdbapi.h

include/ncbi/mmdblocl.h
include/ncbi/motif.h
include/ncbi/ncbi.h
include/ncbi/ncbi_skew_guard.h
include/ncbi/ncbibs.h
include/ncbi/ncbidraw.h
include/ncbi/ncbienv.h

include/ncbi/netlib.h
include/ncbi/netpriv.h
include/ncbi/netscape.h
include/ncbi/ni_defin.h
include/ncbi/ni_error.h
include/ncbi/ni_lib.h
include/ncbi/ni_lib_.h
include/ncbi/ni_net.h
include/ncbi/ni_types.h
include/ncbi/nlm_linear_algebra.h
include/ncbi/objacces.h

include/ncbi/objtax1.h
include/ncbi/objtax3.h
include/ncbi/objtseq.h
include/ncbi/objvalid.h
include/ncbi/odlbox.h
include/ncbi/optimize_target_freq.h
include/ncbi/panels.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/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/urlquery.h
include/ncbi/utilpars.h
include/ncbi/utilpub.h
include/ncbi/valapi.h
include/ncbi/valdlg.h
include/ncbi/valid.h
include/ncbi/validatr.h
include/ncbi/validerr.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

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

%%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%%/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/genbank.png
%%PORTDOCS%%%%DOCSDIR%%/images/graphic.png
%%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png
%%PORTDOCS%%%%DOCSDIR%%/images/logo.png
%%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
%%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png
%%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png

%%PORTDOCS%%%%DOCSDIR%%/images/update.png
%%PORTDOCS%%%%DOCSDIR%%/images/validate.png
%%PORTDOCS%%%%DOCSDIR%%/images/welcome.png
%%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/entrez2.1
%%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.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/formatrpsdb.1
%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.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/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
%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
%%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile
%%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/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

%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html
%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml
%%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif
%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
%%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF
%%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml
%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css

%%DATADIR%%/16SCore.nhr
%%DATADIR%%/16SCore.nin
%%DATADIR%%/16SCore.nsq
%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nhr
%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nin
%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nsq
%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nhr
%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nin
%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nsq
%%DATADIR%%/BLOSUM45
%%DATADIR%%/BLOSUM50
%%DATADIR%%/BLOSUM62

%%DATADIR%%/KSchoth.flt
%%DATADIR%%/KSesigc.mat
%%DATADIR%%/KSesigl.mat
%%DATADIR%%/PAM250
%%DATADIR%%/KSgc.flt
%%DATADIR%%/KShopp.flt
%%DATADIR%%/KSkyte.flt

%%DATADIR%%/LSURef_93.fasta.nhr
%%DATADIR%%/LSURef_93.fasta.nin
%%DATADIR%%/LSURef_93.fasta.nsq
%%DATADIR%%/PAM250
%%DATADIR%%/PAM30
%%DATADIR%%/PAM70
%%DATADIR%%/SSURef_93.fasta.nhr

%%DATADIR%%/UniVec_Core.nin
%%DATADIR%%/UniVec_Core.nsq
%%DATADIR%%/asn2ff.prt
%%DATADIR%%/autofix.prt
%%DATADIR%%/blast.prt
%%DATADIR%%/bstdt.prt
%%DATADIR%%/bstdt.val

%%DATADIR%%/gc.val
%%DATADIR%%/humrep.fsa
%%DATADIR%%/institution_codes.txt
%%DATADIR%%/lat_lon_country.txt
%%DATADIR%%/lat_lon_island.txt
%%DATADIR%%/lat_lon_water.txt
%%DATADIR%%/lineages.txt
%%DATADIR%%/makerpt.prt
%%DATADIR%%/ncbiendo.dat

%%DATADIR%%/ncbiren.dat
%%DATADIR%%/ncbirnam.dat
%%DATADIR%%/objprt.prt
%%DATADIR%%/organelle_products.prt
%%DATADIR%%/product_rules.prt
%%DATADIR%%/pubkey.enc
%%DATADIR%%/rRNA_blast.nal
%%DATADIR%%/rRNAstrand.nal

%%DATADIR%%/sequin.hlp
%%DATADIR%%/sgmlbb.ent
%%DATADIR%%/taxlist.txt
%%DATADIR%%/validrules.prt
@dirrmtry %%DATADIR%%
@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%%/images
%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm lib/ncbi
@dirrm include/ncbi/connect
@dirrm include/ncbi

Return to bug 176544

Lines 2-19 Link Here

(-)biology/ncbi-toolkit/Makefile (-39 / +48 lines)
2	# $FreeBSD: head/biology/ncbi-toolkit/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $	2	# $FreeBSD: head/biology/ncbi-toolkit/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $
3		3
4	PORTNAME= ncbi-toolkit	4	PORTNAME= ncbi-toolkit
5	PORTVERSION= 2009.03.01 # containing BLAST v2.2.19	5	PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
6	PORTREVISION= 1
7	CATEGORIES= biology	6	CATEGORIES= biology
8	MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/	7	MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
9	DISTNAME= ncbi	8	DISTNAME= ncbi
10	DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}	9	DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
11		10
12	MAINTAINER= ports@FreeBSD.org	11	MAINTAINER= ports@FreeBSD.org
13	COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support	12	COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
14		13
		14	OPTIONS_DEFINE= DOCS
		15
15	USE_MOTIF= yes	16	USE_MOTIF= yes
16	CPIO_ARGS= --quiet -pdum -R	17	MAKE_JOBS_UNSAFE= yes
		18
17	SUB_FILES= pkg-message	19	SUB_FILES= pkg-message
18		20
19	# These are the executables we install.	21	# These are the executables we install.
Lines 28-59 Link Here
28	# change in the future with the addition of selectable knobs or	30	# change in the future with the addition of selectable knobs or
29	# new slave ports	31	# new slave ports
30		32
31	TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \	33	TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
32	debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \	34	checksub debruijn demo_regexp demo_regexp_grep dosimple \
33	idfetch indexpub makeset tbl2asn vecscreen demo_regexp \	35	entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
34	demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp	36	gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
		37	vecscreen
35	BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \	38	BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \
36	fastacmd formatdb formatrpsdb impala makemat megablast \	39	fastacmd formatdb formatrpsdb impala makemat megablast \
37	rpsblast seedtop taxblast	40	rpsblast seedtop taxblast
38	X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv	41	X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv
39		42
40	# and these are the man pages we have	43	# and these are the man pages we have
41	MAN1= Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \	44	MAN1= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
42	asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \	45	asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
43	cdscan.1 checksub.1 copymat.1 ddv.1 \	46	copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
44	debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \	47	fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
45	fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \	48	getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
46	idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \	49	taxblast.1 tbl2asn.1 udv.1 vecscreen.1
47	tbl2asn.1 udv.1 vecscreen.1	50
48		51	MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
49	MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \	52	blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
50	blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \	53	blast.1 seedtop.1 blast.1 rpsblast.1
51	blast.1 seedtop.1 blast.1 rpsblast.1	54
		55	.include <bsd.port.options.mk>
52		56
53	post-patch:	57	post-patch:
54	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \	58	@${REINPLACE_CMD} -e \
55	${WRKSRC}/make/makedis.csh \	59	's\|/usr/X11R6\|${LOCALBASE}\|g' ${WRKSRC}/make/makedis.csh
56	${WRKSRC}/platform/freebsd.ncbi.mk	60	@${REINPLACE_CMD} -e \
		61	'/^NCBI_CC/s\|=.*\|= ${CC}\| ; \
		62	/^NCBI_LDFLGS1/s\|=.*\|= ${LDFLAGS}\| ; \
		63	/^NCBI_OPTFLAG/s\|= .*\|= ${CFLAGS}\| ; \
		64	s\|-I/usr/X11R6/include\|\|g ; \
		65	s\|-L/usr/X11R6/lib\|\|g ; \
		66	s\|/usr/local\|${LOCALBASE}\|g ; \
		67	s\|-Wl,-Bstatic\|\| ; \
		68	s\|-Wl,-Bdynamic\|\|' ${WRKSRC}/platform/freebsd.ncbi.mk
57		69
58	# the ncbi-toolkit provides a shell script to drive the build	70	# the ncbi-toolkit provides a shell script to drive the build
59	# and we use it	71	# and we use it
Lines 68-103 Link Here
68	.for blastexe in ${BLAST_EXE}	80	.for blastexe in ${BLAST_EXE}
69	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)	81	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)
70	.endfor	82	.endfor
71
72	.for toolkitexe in ${TOOLKIT_EXE}	83	.for toolkitexe in ${TOOLKIT_EXE}
73	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)	84	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)
74	.endfor	85	.endfor
75
76	.for x11exe in ${X11_EXE}	86	.for x11exe in ${X11_EXE}
77	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)	87	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)
78	.endfor	88	.endfor
79
80	@${MKDIR} ${PREFIX}/lib/${DISTNAME}	89	@${MKDIR} ${PREFIX}/lib/${DISTNAME}
81	(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})	90	(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})
		91	@${MKDIR} ${PREFIX}/include/${DISTNAME}
		92	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
		93	${PREFIX}/include/${DISTNAME})
82	@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect	94	@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
83	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME})	95	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
84	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect)	96	${PREFIX}/include/${DISTNAME}/connect)
85
86	.for man in ${MAN1}	97	.for man in ${MAN1}
87	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)	98	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1)
88	.endfor	99	.endfor
89
90	post-install:
91	@${MKDIR} ${DATADIR}	100	@${MKDIR} ${DATADIR}
92	(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})	101	(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR})
93		102	.if ${PORT_OPTIONS:MDOCS}
94	.if !defined(NOPORTDOCS)
95	@${MKDIR} ${DOCSDIR}	103	@${MKDIR} ${DOCSDIR}
96	(cd ${WRKSRC}/doc && ${FIND} * \| ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})	104	@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) \| \
97	.endif	105	(cd ${DOCSDIR} && ${TAR} --unlink -xf -)
98		106	@${FIND} ${DOCSDIR} \| ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
99	.if !defined(BATCH)	107	@${FIND} ${DOCSDIR} -type d \| ${XARGS} ${CHMOD} a+rx
100	@ ${CAT} ${PKGMESSAGE}	108	@${FIND} ${DOCSDIR} -type f \| ${XARGS} ${CHMOD} ${SHAREMODE}
101	.endif	109	.endif
		110	@${CAT} ${PKGMESSAGE}
102		111
103	.include <bsd.port.mk>	112	.include <bsd.port.mk>

Lines 8-14 Link Here

(-)biology/ncbi-toolkit/files/patch-make-makenet.unx (-8 / +8 lines)
8	SEQUIN_OPTS =	8	SEQUIN_OPTS =
9	LIBCOPY = cp -p	9	LIBCOPY = cp -p
10	SRCCOPY = ./ln-if-absent	10	SRCCOPY = ./ln-if-absent
11	@@ -923,17 +924,17 @@	11	@@ -934,17 +935,17 @@
12	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \	12	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
13	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \	13	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
14	$(LIBCOMPADJ) $(LIB2) $(LIB1) \	14	$(LIBCOMPADJ) $(LIB2) $(LIB1) \
Lines 17-35 Link Here
17		17
18	udv : $(OBJUDV)	18	udv : $(OBJUDV)
19	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \	19	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
20	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \	20	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
21	$(LIB23) $(LIBCOMPADJ) $(LIB2) \	21	$(LIB23) $(LIBCOMPADJ) $(LIB2) \
22	- $(LIB1) $(VIBLIBS) $(OTHERLIBS)	22	- $(LIB1) $(VIBLIBS) $(OTHERLIBS)
23	+ $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)	23	+ $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
24		24
25	Nentrez : entrez.c $(ULIB31)	25	Nentrez : entrez.c $(ULIB31)
26	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \	26	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
27	- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)	27	- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
28	+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)	28	+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
29		29
30	# left this in (Tentrez) for script backwards compatibility	30	# left this in (Tentrez) for script backwards compatibility
31	Tentrez : entrez.c $(ULIB31)	31	Tentrez : entrez.c $(ULIB31)
32	@@ -1114,7 +1115,7 @@	32	@@ -1140,7 +1141,7 @@
33	entrez2 : entrez2.c	33	entrez2 : entrez2.c
34	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \	34	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
35	$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \	35	$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
Lines 38-44 Link Here
38	$(VIB_POST_LINK) entrez2	38	$(VIB_POST_LINK) entrez2
39		39
40	# demo program (spidey)	40	# demo program (spidey)
41	@@ -1383,7 +1384,7 @@	41	@@ -1421,7 +1422,7 @@
42	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \	42	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
43	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \	43	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
44	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \	44	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
Lines 47-53 Link Here
47	$(VIB_POST_LINK) Psequin	47	$(VIB_POST_LINK) Psequin
48		48
49	# 'sbtedit' Submission Template Editor	49	# 'sbtedit' Submission Template Editor
50	@@ -1395,7 +1396,7 @@	50	@@ -1433,7 +1434,7 @@
51	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \	51	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
52	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \	52	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
53	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \	53	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
Lines 55-58 Link Here
55	+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)	55	+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
56	$(VIB_POST_LINK) sbtedit	56	$(VIB_POST_LINK) sbtedit
57		57
58	salogif.o: salogif.c	58	# 'streamer' Sequinesque Stream Editor