5081af2c64
assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
67 lines
1.8 KiB
Makefile
67 lines
1.8 KiB
Makefile
# New ports collection makefile for: phred
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# Date created: 6 December 2007
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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= phred
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PORTVERSION= 0.020425.c
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CATEGORIES= biology
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MASTER_SITES= # put the tarball manually
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DISTNAME= ${PORTNAME}-dist-${PORTVERSION:S/0.//}-acd
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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= Base calling and quality value assignment on DNA sequencing
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RESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
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NO_WRKSUBDIR= yes
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ALL_TARGET= phred daev
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BINMODE= 0111 # avoid copying binaries as required by the agreement
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BINARIES= phred daev
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.for f in ${BINARIES}
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PLIST_FILES+= bin/${f}
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.endfor
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DATADIR= ${PREFIX}/etc/PhredPar
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DATAFILES= phredpar.dat
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.for f in ${DATAFILES}
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PORTDATA+= ${f}.dist
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.endfor
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PORTDOCS= NEWS PHRED.DOC DAEV.DOC
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.include <bsd.port.pre.mk>
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.for f in ${DISTFILES}
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.if !exists(${DISTDIR}/${f})
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IGNORE= you must request the source code \(${f}\) via e-mail, place it manually in ${DISTDIR}, and then try it again
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.endif
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.endfor
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do-install:
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.for f in ${BINARIES}
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@${INSTALL_PROGRAM} ${WRKSRC}/${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} ${WRKSRC}/${f} ${DATADIR}/${f}.dist
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.endfor
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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} ${DOCSDIR}
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.endfor
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.endif
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@${ECHO} "---------------------------------------------------------------------------"
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@${ECHO} "You must set PHRED_PARAMETER_FILE environment variable."
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@${ECHO} ""
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@${ECHO} "The default parameter file in the distribution is located at:"
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@${ECHO} " ${DATADIR}/phredpar.dat.dist"
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@${ECHO} "---------------------------------------------------------------------------"
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.include <bsd.port.post.mk>
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