biology/paml: update to version 4.9c and various improvements
- Update to version 4.9c - Set LICENSE=GPLv3 - Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@). - Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball. - Fix broken permissions. - Delete Windows executables. - Build and install useful binaries not built by upstream's Makefile. - Update pkg-descr. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8040
This commit is contained in:
Joseph Mingrone
parent
29a8954d58
commit
512daaacda
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=422846
@ -2,7 +2,7 @@
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# $FreeBSD$
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PORTNAME= paml
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PORTVERSION= 4.9a
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PORTVERSION= 4.9c
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CATEGORIES= biology
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MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
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DISTNAME= ${PORTNAME}${PORTVERSION}
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@ -10,24 +10,52 @@ DISTNAME= ${PORTNAME}${PORTVERSION}
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MAINTAINER= jrm@FreeBSD.org
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COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
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USES= gmake tar:tgz
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WRKSRC= ${WRKDIR}/${DISTNAME}/src
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MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
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LICENSE= GPLv3
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BINARIES= baseml basemlg chi2 codeml evolver pamp yn00
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DOC_FILES= pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
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USES= gmake tar:tgz
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BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \
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evolverNSbranchsites evolverNSsites pamp yn00
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PORTDOCS= MCMCtree.Tutorials.pdf MCMCtreeDOC.pdf pamlDOC.pdf pamlFAQs.pdf \
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pamlHistory.txt README.txt
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DATA= 3s.trees 4s.trees 5s.trees 6s.trees GeneticCode.txt MCaa.dat \
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MCbase.dat MCbaseRandomTree.dat MCcodon.dat aaml.ctl baseml.ctl \
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brown.nuc brown.rooted.trees brown.trees codeml.ctl codonml.ctl \
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mcmctree.ctl pamp.ctl paupblock paupend paupstart stewart.aa \
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stewart.trees yn00.ctl
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PORTDATA= ${DATA} dat examples Technical
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OPTIONS_DEFINE= DOCS
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# Fix broken permissions and remove Windows executables
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post-extract:
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@${CHMOD} -R a+rX ${WRKDIR}
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@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
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do-build:
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@cd ${WRKSRC}/src && \
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${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} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin
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${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
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.endfor
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@${MKDIR} ${STAGEDIR}${DATADIR}
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.for f in ${DATA}
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${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}/${DATADIR}
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.endfor
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(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat examples Technical" \
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${STAGEDIR}/${DATADIR})
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do-install-DOCS-on:
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@${MKDIR} ${STAGEDIR}${DOCSDIR}
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.for f in ${DOC_FILES}
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${INSTALL_DATA} ${WRKSRC}/../doc/${f} ${STAGEDIR}${DOCSDIR}
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.endfor
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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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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1463365805
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SHA256 (paml4.9a.tgz) = 1400b6a48aa7ba2dee637352430a1f64594674168cf7a749ac79093da9a39ef4
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SIZE (paml4.9a.tgz) = 5853303
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TIMESTAMP = 1474920596
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SHA256 (paml4.9c.tgz) = c0c5fb1e1af5a27b2bd80c9daaa91c259157f34a44d297e058f1b9d8689dce02
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SIZE (paml4.9c.tgz) = 5405921
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@ -1,22 +1,9 @@
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Phylogenetic Analysis by Maximum Likelihood (PAML)
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PAML is a program package for phylogenetic analyses of DNA or protein
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sequences using maximum likelihood, and is maintained and distributed
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by Ziheng Yang.
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Possible uses of the programs are:
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- Estimation of branch lengths in a phylogenetic tree and parameters
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in the evolutionary model such as the transition/transversion rate
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ratio, the shape parameter of the gamma distribution for variable
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evolutionary rates among sites, and rate parameters for different
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genes;
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- Test of hypotheses concerning sequence evolution, such as rate
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constancy and independence among nucleotide or amino acid sites, rate
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constancy among lineages (the molecular clock), and homogeneity of
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evolutionary process in multiple genes;
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- Calculation of substitution rates at sites;
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- Reconstruction of ancestral nucleotide or amino acid sequences;
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- Simulation of nucleotide, codon, and amino acid sequence data sets;
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- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
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PAML is a package of programs for phylogenetic analyses of DNA or protein
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sequences using maximum likelihood. It is not good for tree making. It may be
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used to estimate parameters and test hypotheses for the study the evolutionary
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process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
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PhyML, or RaxML.
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WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
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@ -3,8 +3,8 @@ bin/basemlg
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bin/chi2
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bin/codeml
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bin/evolver
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bin/evolverNSbranches
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bin/evolverNSbranchsites
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bin/evolverNSsites
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bin/pamp
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bin/yn00
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%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
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%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
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%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
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