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0263b9d868
both current (fc4) and future linux (f8) distributions at one ports tree. The patch contains full changes to ports/Mk files and all ports involved. But only infrastructure is changed. The resulting packages are the same as before. Hence no need to bump PORTREVISIONs. The idea was taken from bsd.gnome.mk and others. More than 130 ports are switched to follow a new linux infrastructure introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new bsd.linux-apps.mk. Thanks for all who was involved and helped me with this work. And help from Alexander Leidinger was incredible. Other changes are coming. Stay tuned! PR: ports/132510 Submitted by: bsam (me) Exp-run by: portmgr (pav)
108 lines
3.2 KiB
Makefile
108 lines
3.2 KiB
Makefile
# New ports collection makefile for: phred
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# Date created: 8 July 2005
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# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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#
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# $FreeBSD$
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#
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PORTNAME= consed
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PORTVERSION= 16.0
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CATEGORIES= biology
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MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/
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DISTNAME= ${PORTNAME}_linux
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EXTRACT_SUFX= .tar.Z
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MAINTAINER= mzaki@biol.s.u-tokyo.ac.jp
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COMMENT= A graphical tool for editing Phrap assemblies
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RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \
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phrap:${PORTSDIR}/biology/phrap \
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phd2fasta:${PORTSDIR}/biology/phd2fasta
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USE_PERL5= yes
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USE_LINUX= yes
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USE_LINUX_APPS= xorglibs
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ONLY_FOR_ARCHS= i386 amd64
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RESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
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.if defined(PACKAGE_BUILDING)
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IGNORE= distribution files must be obtained via the authors
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.endif
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NO_WRKSUBDIR= yes
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BUILD_WRKSRC= ${WRKSRC}/misc/mktrace
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ALL_TARGET= mktrace
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BINARIES= consed mktrace sffinfo sff2scf
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CONTRIBS= ace2OligosWithComments.perl ace2fof \
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aceContigs2Phds.perl acestatus.pl export_cons \
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mergeAces.perl recover_consensus_tags revert_fof
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SCRIPTS= ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \
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amplifyTranscripts.perl catPhdFiles.perl \
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countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \
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findSequenceMatchesForConsed.perl lib2Phd.perl \
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orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \
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revertToUneditedRead tagRepeats.perl transferConsensusTags.perl
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.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS}
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PLIST_FILES+= bin/${f}
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.endfor
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DATADIR= ${PREFIX}/lib/screenLibs
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DATAFILES= primerCloneScreen.seq primerSubcloneScreen.seq \
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repeats.fasta singleVectorForRestrictionDigest.fasta
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NULLFILES= vector.seq
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.for f in ${DATAFILES} ${NULLFILES}
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PORTDATA+= ${f}.dist
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.endfor
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PORTDOCS= README.txt
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.if defined(WITH_EXAMPLES)
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EXAMPLES= standard autofinish assembly_view polyphred
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PLIST= ${PKGDIR}/pkg-plist.examples
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.endif
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post-build:
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(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
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(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)
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do-install:
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@${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed
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@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/
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@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/
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@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/
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.for f in ${BINARIES}
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@${CHMOD} a-r ${PREFIX}/bin/${f}
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.endfor
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.for f in ${CONTRIBS}
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@${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/
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.endfor
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.for f in ${SCRIPTS}
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@${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/
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.endfor
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@${MKDIR} ${DATADIR}
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.for f in ${DATAFILES}
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@${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist
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.endfor
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.for f in ${NULLFILES}
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@${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist
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.endfor
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.if !defined(NOPORTEXAMPLES)
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@${MKDIR} ${EXAMPLESDIR}
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.for dir in ${EXAMPLES}
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@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
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.endfor
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.endif
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.if !defined(NOPORTDOCS)
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@${MKDIR} ${DOCSDIR}
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.for f in ${PORTDOCS}
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@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
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.endfor
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.endif
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.if !defined(WITH_EXAMPLES)
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@${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them."
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.endif
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@${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'"
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.include <bsd.port.mk>
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