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# Created by: tonym
# $FreeBSD$
PORTNAME= ncbi-toolkit
PORTVERSION= 2009.03.01 # containing BLAST v2.2.19
PORTREVISION= 1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.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
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= 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>
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