Index: head/biology/paml/Makefile =================================================================== --- head/biology/paml/Makefile (revision 468296) +++ head/biology/paml/Makefile (revision 468297) @@ -1,61 +1,53 @@ # Created by: dbader@eece.unm.edu # $FreeBSD$ PORTNAME= paml -PORTVERSION= 4.9c -PORTREVISION= 1 +DISTVERSION= 4.9h CATEGORIES= biology MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/ -DISTNAME= ${PORTNAME}${PORTVERSION} +DISTNAME= ${PORTNAME}${DISTVERSION} MAINTAINER= jrm@FreeBSD.org COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML) LICENSE= GPLv3 -USES= gmake tar:tgz +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 -PORTDOCS= MCMCtree.Tutorials.pdf MCMCtreeDOC.pdf pamlDOC.pdf pamlFAQs.pdf \ - pamlHistory.txt README.txt +OPTIONS_DEFINE= DOCS EXAMPLES -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= ${DATA} dat examples Technical - -OPTIONS_DEFINE= DOCS - -# Remove Windows executables post-extract: @${FIND} ${WRKSRC}/Technical -name "*.exe" -delete do-build: - @cd ${WRKSRC}/src && \ - ${SETENV} ${MAKE_ENV} ${MAKE_CMD} + @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} + +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 Index: head/biology/paml/distinfo =================================================================== --- head/biology/paml/distinfo (revision 468296) +++ head/biology/paml/distinfo (revision 468297) @@ -1,3 +1,3 @@ -TIMESTAMP = 1475182775 -SHA256 (paml4.9c.tgz) = 8be4250399f3daaf22b0b643fa1a1fd5fddb892d54ce330bfe77ea9dbed577b9 -SIZE (paml4.9c.tgz) = 5409741 +TIMESTAMP = 1524675240 +SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3 +SIZE (paml4.9h.tgz) = 6241149 Index: head/biology/paml/pkg-plist =================================================================== --- head/biology/paml/pkg-plist (revision 468296) +++ head/biology/paml/pkg-plist (revision 468297) @@ -1,10 +1,172 @@ +%%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf +%%PORTDOCS%%%%DOCSDIR%%/README.txt +%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf +%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf +%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl bin/baseml bin/basemlg bin/chi2 bin/codeml bin/evolver bin/evolverNSbranches bin/evolverNSbranchsites bin/evolverNSsites bin/pamp bin/yn00