# ex:ts=8
# New ports collection makefile for:	NCBI
# Date created:         03 April 2000
# Whom:                 tonym
#
# $FreeBSD$
#

PORTNAME=	ncbi-toolkit
PORTVERSION=	2009.03.01	# containing BLAST v2.2.19
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME=	ncbi
DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}

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
SUB_FILES=	pkg-message

# These are the executables we install.
#
# 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 asn2idx asn2xml asndhuff asntool checksub \
		debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \
		idfetch indexpub makeset tbl2asn vecscreen demo_regexp \
		demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp
BLAST_EXE=	bl2seq blastall blastcl3 blastclust blastpgp copymat \
		fastacmd formatdb formatrpsdb impala makemat megablast \
		rpsblast seedtop taxblast
X11_EXE=	Nentrez Psequin ddv entrez2 sbtedit udv

# and these are the man pages we have
MAN1=	asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1	asn2xml.1 \
	asndhuff.1 asnval.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
	copymat.1 ddv.1 debruijn.1 errhdr.1 fa2htgs.1 fastacmd.1 \
	findspl.1 fmerge.1 formatdb.1 getmesh.1 getpub.1 gil2bin.1 \
	idfetch.1 indexpub.1 makemat.1 makeset.1 sbtedit.1 tbl2asn.1 \
	udv.1 vecscreen.1 Psequin.1 asn2all.1 asntool.1 entrez2.1 \
	formatrpsdb.1
MAN1=	Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \
	asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \
	cdscan.1 checksub.1 copymat.1 ddv.1 \
	debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
	fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \
	idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \
	tbl2asn.1 udv.1 vecscreen.1

MLINKS=	blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
	blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
	blast.1 seedtop.1 blast.1 rpsblast.1

post-patch:
	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
		${WRKSRC}/make/makedis.csh \
		${WRKSRC}/platform/freebsd.ncbi.mk

# 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_DATA} *.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}
	(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})

.if !defined(NOPORTDOCS)
	@${MKDIR} ${DOCSDIR}
	(cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
.endif

.if !defined(BATCH)
	@ ${CAT} ${PKGMESSAGE}
.endif

.include <bsd.port.mk>