1 files changed, 72 insertions, 23 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>