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# Created by: tonym
# $FreeBSD$
PORTNAME= ncbi-toolkit
PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
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
USES= iconv motif
MAKE_JOBS_UNSAFE= yes
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 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
MAN_FILES= 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
MAN_LINKS= bl2seq blastall blastcl3 blastpgp impala megablast \
seedtop rpsblast
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||' ${WRKSRC}/platform/freebsd.ncbi.mk
@${REINPLACE_CMD} -e 's/%%ICONV_LIB%%/${ICONV_LIB}/' \
${WRKSRC}/make/makeall.unx ${WRKSRC}/make/makenet.unx
# 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:
(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${BLAST_EXE} \
${TOOLKIT_EXE} ${X11_EXE} ${STAGEDIR}${PREFIX}/bin)
@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${DISTNAME}
(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \
${STAGEDIR}${PREFIX}/lib/${DISTNAME})
@${MKDIR} ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME})
(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect)
(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${MAN_FILES} \
${STAGEDIR}${MANPREFIX}/man/man1)
.for man in ${MAN_LINKS}
${LN} -s ${MANPREFIX}/man/man1/blast.1.gz \
${STAGEDIR}${PREFIX}/man/man1/${man}.1.gz
.endfor
@${MKDIR} ${STAGEDIR}${DATADIR}
(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR})
@${MKDIR} ${STAGEDIR}${DOCSDIR}
@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
(cd ${STAGEDIR}${DOCSDIR} && ${TAR} --unlink -xf -)
@${FIND} ${STAGEDIR}${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
@${FIND} ${STAGEDIR}${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
.include <bsd.port.mk>
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