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110a0bfa20
- Remove BROKEN=. Version 4.9i became unfetchable when the author pulled
the tarball to prevent users from downloading a version with new, serious
bugs.
Upstream changes described by the author:
- mcmctree: Initial values have ages that are too old, exceeding max
bounds. In theory bounds in mcmctree are always soft so that the node
ages will move to the area of posterior mode when burnin is long enough.
In practice the poor starting values are problematic and requires long
burn-in. I have rewritten the code for generating initial values to
respect the min and max bounds specified in the fossil calibrations.
- codeml: A bug introduced in 4.9i caused the clade labels ($) to be
ignored. This affects the branch, branch-site and clade models. If
your tree has branch labels (#) only and no clade models, everything
will be fine. If you have used the clade label ($) in the tree with or
without the branch label (#), either the program will abort or the
results will be incorrect. The clade label ($) is supposed to label
all branches in the clade as well as the branch itself, but all clade
labels in the tree are ignored in 4.9i. Earlier versions are correct.
55 lines
1.5 KiB
Makefile
55 lines
1.5 KiB
Makefile
# Created by: dbader@eece.unm.edu
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# $FreeBSD$
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PORTNAME= paml
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PORTVERSION= 4.9j
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CATEGORIES= biology
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MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
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DISTNAME= ${PORTNAME}${DISTVERSION}
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MAINTAINER= jrm@FreeBSD.org
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COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
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LICENSE= GPLv3
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USES= dos2unix gmake tar:tgz
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DOS2UNIX_GLOB= *.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
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*.trees *.txt *.xml paupblock paupend
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BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \
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evolverNSbranchsites evolverNSsites pamp yn00
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OPTIONS_DEFINE= DOCS EXAMPLES
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post-extract:
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@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
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do-build:
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@cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
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.for f in NSbranches NSsites NSbranchsites
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@cd ${WRKSRC}/src && \
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${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
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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} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
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.endfor
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do-install-DOCS-on:
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@${MKDIR} ${STAGEDIR}${DOCSDIR}
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${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
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${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
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do-install-EXAMPLES-on:
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@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
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(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
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${STAGEDIR}${EXAMPLESDIR})
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(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
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.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
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${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
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.endfor
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.include <bsd.port.mk>
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