9da018b5cc
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml Major changes include: blastall now uses the new engine by default, resulting in significant performance improvements and enabling query concatenation for all program types. PR: ports/98570 Submitted by: maintainer Approved by: lawrance (mentor, implict)
100 lines
3.3 KiB
Makefile
100 lines
3.3 KiB
Makefile
# ex:ts=8
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# New ports collection makefile for: NCBI
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# Date created: 03 April 2000
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# Whom: tonym
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#
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# $FreeBSD$
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#
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PORTNAME= ncbi-toolkit
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PORTVERSION= 2006.05.07 # containing BLAST v2.2.14
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.ncbi.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= fernan@iib.unsam.edu.ar
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COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
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USE_MOTIF= yes
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CPIO_ARGS= --quiet -pdum -R
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PKGMESSAGE= ${WRKDIR}/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 checksub \
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debruijn entrcmd fa2htgs findspl getseq getfeat getmesh \
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getpub gil2bin idfetch indexpub makeset tbl2asn vecscreen
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BLAST_EXE= bl2seq blast blastall blastcl3 blastclust blastpgp copymat \
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fastacmd formatdb impala makemat megablast rpsblast seedtop
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X11_EXE= Nentrez Psequin ddv entrez2 netentcf sbtedit udv
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# and these are the man pages we have
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MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \
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asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \
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debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
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fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \
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idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.1 \
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tbl2asn.1 udv.1 vecscreen.1
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MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
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blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
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blast.1 seedtop.1
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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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.for blastexe in ${BLAST_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)
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.endfor
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.for toolkitexe in ${TOOLKIT_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)
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.endfor
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.for x11exe in ${X11_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)
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.endfor
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@${MKDIR} ${PREFIX}/lib/${DISTNAME}
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(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})
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@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
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(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME})
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(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect)
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.for man in ${MAN1}
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(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)
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.endfor
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post-install:
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@${MKDIR} ${DATADIR}
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(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})
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.if !defined(NOPORTDOCS)
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@${MKDIR} ${DOCSDIR}
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(cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
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.endif
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.if !defined(BATCH)
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@ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${FILESDIR}/pkg-message.in > ${PKGMESSAGE}
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@ ${CAT} ${PKGMESSAGE}
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.endif
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.include <bsd.port.mk>
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