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sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
90 lines
2.4 KiB
Makefile
90 lines
2.4 KiB
Makefile
# New ports collection makefile for: velvet
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# Date created: 27 Oct 2009
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# Whom: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
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#
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# $FreeBSD$
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#
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PORTNAME= velvet
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PORTVERSION= 0.7.55
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CATEGORIES= biology
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MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/
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DISTNAME= ${PORTNAME}_${PORTVERSION}
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EXTRACT_SUFX= .tgz
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MAINTAINER= mzaki@m.u-tokyo.ac.jp
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COMMENT= Sequence assembler for very short reads
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USE_GMAKE= yes
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ALL_TARGET= default
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MAXKMERLENGTH?= 31
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MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH}
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USE_PERL5_RUN= yes
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BINARIES= velvetg velveth
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SCRIPTS= contrib/VelvetOptimiser/VelvetOptimiser.pl \
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contrib/afg_handling/asmbly_splitter.pl \
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contrib/afg_handling/snp_view.pl \
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contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
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contrib/fasta2agp/fasta2agp.pl \
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contrib/extractContigReads/extractContigReads.pl \
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contrib/observed-insert-length.pl/observed-insert-length.pl \
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contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl
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PERLMOD_DIRS= contrib/VelvetOptimiser/VelvetOpt
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PERLMOD_FILES= contrib/VelvetOptimiser/VelvetOpt/Assembly.pm \
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contrib/VelvetOptimiser/VelvetOpt/Utils.pm \
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contrib/VelvetOptimiser/VelvetOpt/gwrap.pm \
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contrib/VelvetOptimiser/VelvetOpt/hwrap.pm
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.if !defined(WITHOUT_PYTHON)
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USE_PYTHON= yes
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SCRIPTS+= contrib/layout/graph2.py
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.endif
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.for f in ${BINARIES} ${SCRIPTS}
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PLIST_FILES+= bin/${f:T}
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.endfor
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.for d in ${PERLMOD_DIRS}
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PLIST_DIRS+= %%SITE_PERL%%/${d:T}
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.endfor
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.for f in ${PERLMOD_FILES}
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PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T}
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.endfor
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PORTDOCS= ChangeLog Manual.pdf
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post-patch:
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.for f in ${SCRIPTS}
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${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
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.endfor
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.if !defined(WITHOUT_PYTHON)
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(IFS=''; ${REINPLACE_CMD} -e `${ECHO} '1i\'; ${ECHO} '#!${PYTHON_CMD}'` ${WRKSRC}/contrib/layout/graph2.py)
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.endif
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post-build:
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${REINPLACE_CMD} -e s,%%MAXKMERLENGTH%%,${MAXKMERLENGTH},g ${WRKSRC}/contrib/VelvetOptimiser/VelvetOptimiser.pl
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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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.for f in ${SCRIPTS}
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${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/${f:T}
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.endfor
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.for d in ${PERLMOD_DIRS}
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${MKDIR} ${PREFIX}/${SITE_PERL_REL}/${d:T}
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.endfor
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.for f in ${PERLMOD_FILES}
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${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T}
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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_MAN} ${WRKSRC}/${f} ${DOCSDIR}
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.endfor
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.endif
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.include <bsd.port.mk>
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