Date: Wed, 28 Sep 2016 02:30:29 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r422846 - head/biology/paml Message-ID: <201609280230.u8S2UTu6013650@repo.freebsd.org>
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Author: jrm Date: Wed Sep 28 02:30:29 2016 New Revision: 422846 URL: https://svnweb.freebsd.org/changeset/ports/422846 Log: 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 Modified: head/biology/paml/Makefile head/biology/paml/distinfo head/biology/paml/pkg-descr head/biology/paml/pkg-plist Modified: head/biology/paml/Makefile ============================================================================== --- head/biology/paml/Makefile Wed Sep 28 02:27:03 2016 (r422845) +++ head/biology/paml/Makefile Wed Sep 28 02:30:29 2016 (r422846) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= paml -PORTVERSION= 4.9a +PORTVERSION= 4.9c CATEGORIES= biology MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/ DISTNAME= ${PORTNAME}${PORTVERSION} @@ -10,24 +10,52 @@ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= jrm@FreeBSD.org COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML) +LICENSE= GPLv3 + USES= gmake tar:tgz -WRKSRC= ${WRKDIR}/${DISTNAME}/src -MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}" -BINARIES= baseml basemlg chi2 codeml evolver pamp yn00 -DOC_FILES= pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt +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} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin + ${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} -.for f in ${DOC_FILES} - ${INSTALL_DATA} ${WRKSRC}/../doc/${f} ${STAGEDIR}${DOCSDIR} -.endfor + ${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR} .include <bsd.port.mk> Modified: head/biology/paml/distinfo ============================================================================== --- head/biology/paml/distinfo Wed Sep 28 02:27:03 2016 (r422845) +++ head/biology/paml/distinfo Wed Sep 28 02:30:29 2016 (r422846) @@ -1,3 +1,3 @@ -TIMESTAMP = 1463365805 -SHA256 (paml4.9a.tgz) = 1400b6a48aa7ba2dee637352430a1f64594674168cf7a749ac79093da9a39ef4 -SIZE (paml4.9a.tgz) = 5853303 +TIMESTAMP = 1474920596 +SHA256 (paml4.9c.tgz) = c0c5fb1e1af5a27b2bd80c9daaa91c259157f34a44d297e058f1b9d8689dce02 +SIZE (paml4.9c.tgz) = 5405921 Modified: head/biology/paml/pkg-descr ============================================================================== --- head/biology/paml/pkg-descr Wed Sep 28 02:27:03 2016 (r422845) +++ head/biology/paml/pkg-descr Wed Sep 28 02:30:29 2016 (r422846) @@ -1,22 +1,9 @@ Phylogenetic Analysis by Maximum Likelihood (PAML) -PAML is a program package for phylogenetic analyses of DNA or protein -sequences using maximum likelihood, and is maintained and distributed -by Ziheng Yang. - -Possible uses of the programs are: -- Estimation of branch lengths in a phylogenetic tree and parameters - in the evolutionary model such as the transition/transversion rate - ratio, the shape parameter of the gamma distribution for variable - evolutionary rates among sites, and rate parameters for different - genes; -- Test of hypotheses concerning sequence evolution, such as rate - constancy and independence among nucleotide or amino acid sites, rate - constancy among lineages (the molecular clock), and homogeneity of - evolutionary process in multiple genes; -- Calculation of substitution rates at sites; -- Reconstruction of ancestral nucleotide or amino acid sequences; -- Simulation of nucleotide, codon, and amino acid sequence data sets; -- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. +PAML is a package of programs for phylogenetic analyses of DNA or protein +sequences using maximum likelihood. It is not good for tree making. It may be +used to estimate parameters and test hypotheses for the study the evolutionary +process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY, +PhyML, or RaxML. WWW: http://abacus.gene.ucl.ac.uk/software/paml.html Modified: head/biology/paml/pkg-plist ============================================================================== --- head/biology/paml/pkg-plist Wed Sep 28 02:27:03 2016 (r422845) +++ head/biology/paml/pkg-plist Wed Sep 28 02:30:29 2016 (r422846) @@ -3,8 +3,8 @@ bin/basemlg bin/chi2 bin/codeml bin/evolver +bin/evolverNSbranches +bin/evolverNSbranchsites +bin/evolverNSsites bin/pamp bin/yn00 -%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf -%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf -%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
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