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104 lines
3.7 KiB
Makefile
104 lines
3.7 KiB
Makefile
# Created by: tonym
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# $FreeBSD$
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PORTNAME= ncbi-toolkit
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PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
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DISTNAME= ncbi
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DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
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MAINTAINER= ports@FreeBSD.org
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COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
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OPTIONS_DEFINE= DOCS
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USES= iconv motif
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MAKE_JOBS_UNSAFE= yes
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SUB_FILES= pkg-message
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# These are the executables we install.
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#
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# We follow Debian in the separation of the port in three
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# main categories and in the selection of programs that
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# are installed in each case. This Makes Sense (TM).
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# Thus, we drop a handful of programs that are useful only as tests
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# or code examples
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# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff)
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# Right now the port installs all the executables below, this may
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# change in the future with the addition of selectable knobs or
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# new slave ports
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TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
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checksub debruijn demo_regexp demo_regexp_grep dosimple \
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entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
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gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
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vecscreen
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BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \
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fastacmd formatdb formatrpsdb impala makemat megablast \
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rpsblast seedtop taxblast
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X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv
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# and these are the man pages we have
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MAN_FILES= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
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asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
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copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
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fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
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getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
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taxblast.1 tbl2asn.1 udv.1 vecscreen.1
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MAN_LINKS= bl2seq blastall blastcl3 blastpgp impala megablast \
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seedtop rpsblast
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post-patch:
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@${REINPLACE_CMD} -e \
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's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
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@${REINPLACE_CMD} -e \
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'/^NCBI_CC/s|=.*|= ${CC}| ; \
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/^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
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/^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
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s|-I/usr/X11R6/include||g ; \
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s|-L/usr/X11R6/lib||g ; \
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s|/usr/local|${LOCALBASE}|g ; \
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s|-Wl,-Bstatic|| ; \
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s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk
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@${REINPLACE_CMD} -e 's/%%ICONV_LIB%%/${ICONV_LIB}/' \
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${WRKSRC}/make/makeall.unx ${WRKSRC}/make/makenet.unx
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# the ncbi-toolkit provides a shell script to drive the build
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# and we use it
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do-build:
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cd ${WRKDIR}; ./${DISTNAME}/make/makedis.csh
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# the ncbi-toolkit does not provide an install target
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# we thus roll our own
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do-install:
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${BLAST_EXE} \
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${TOOLKIT_EXE} ${X11_EXE} ${STAGEDIR}${PREFIX}/bin)
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@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${DISTNAME}
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(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \
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${STAGEDIR}${PREFIX}/lib/${DISTNAME})
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@${MKDIR} ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
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(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
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${STAGEDIR}${PREFIX}/include/${DISTNAME})
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(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
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${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect)
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(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${MAN_FILES} \
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${STAGEDIR}${MANPREFIX}/man/man1)
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.for man in ${MAN_LINKS}
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${LN} -s ${MANPREFIX}/man/man1/blast.1.gz \
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${STAGEDIR}${PREFIX}/man/man1/${man}.1.gz
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.endfor
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@${MKDIR} ${STAGEDIR}${DATADIR}
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(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR})
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@${MKDIR} ${STAGEDIR}${DOCSDIR}
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@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
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(cd ${STAGEDIR}${DOCSDIR} && ${TAR} --unlink -xf -)
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@${FIND} ${STAGEDIR}${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
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@${FIND} ${STAGEDIR}${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
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.include <bsd.port.mk>
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