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# Created by: dbader@eece.unm.edu
PORTNAME= paml
PORTVERSION= 4.9j
CATEGORIES= biology
MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
DISTNAME= ${PORTNAME}${DISTVERSION}
MAINTAINER= jrm@FreeBSD.org
COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
LICENSE= GPLv3
USES= dos2unix gmake tar:tgz
DOS2UNIX_GLOB= *.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
*.trees *.txt *.xml paupblock paupend
BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \
evolverNSbranchsites evolverNSsites pamp yn00
OPTIONS_DEFINE= DOCS EXAMPLES
post-extract:
@${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
do-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
do-install-EXAMPLES-on:
@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
${STAGEDIR}${EXAMPLESDIR})
(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
.endfor
.include <bsd.port.mk>
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