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# Created by: dbader@eece.unm.edu
# $FreeBSD$
PORTNAME= paml
PORTVERSION= 4.9c
PORTREVISION= 1
CATEGORIES= biology
MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
DISTNAME= ${PORTNAME}${PORTVERSION}
MAINTAINER= jrm@FreeBSD.org
COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
LICENSE= GPLv3
USES= gmake tar:tgz
BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \
evolverNSbranchsites evolverNSsites pamp yn00
PORTDOCS= MCMCtree.Tutorials.pdf MCMCtreeDOC.pdf pamlDOC.pdf pamlFAQs.pdf \
pamlHistory.txt README.txt
DATA= 3s.trees 4s.trees 5s.trees 6s.trees GeneticCode.txt MCaa.dat \
MCbase.dat MCbaseRandomTree.dat MCcodon.dat aaml.ctl baseml.ctl \
brown.nuc brown.rooted.trees brown.trees codeml.ctl codonml.ctl \
mcmctree.ctl pamp.ctl paupblock paupend paupstart stewart.aa \
stewart.trees yn00.ctl
PORTDATA= ${DATA} dat examples Technical
OPTIONS_DEFINE= DOCS
# Fix broken permissions and remove Windows executables
post-extract:
@${CHMOD} -R a+rX ${WRKDIR}
@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
do-build:
@cd ${WRKSRC}/src && \
${SETENV} ${MAKE_ENV} ${MAKE_CMD}
.for f in NSbranches NSsites NSbranchsites
@cd ${WRKSRC}/src && \
${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
.endfor
do-install:
.for f in ${BINARIES}
${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
.endfor
@${MKDIR} ${STAGEDIR}${DATADIR}
.for f in ${DATA}
${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}/${DATADIR}
.endfor
(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat examples Technical" \
${STAGEDIR}/${DATADIR})
do-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
.include <bsd.port.mk>
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