diff --git a/biology/paml/Makefile b/biology/paml/Makefile index a8c84d9fb60c..d0f49022b3f7 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -1,51 +1,49 @@ PORTNAME= paml -PORTVERSION= 4.9j +DISTVERSIONPREFIX= v +DISTVERSION= 4.10.5 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 \ +USES= dos2unix gmake +DOS2UNIX_GLOB= *.aa *.c *.ctl *.dat *.HKYG5 *.nexus *.nuc *.phy *.result *.tre \ *.trees *.txt *.xml paupblock paupend +USE_GITHUB= yes +GH_ACCOUNT= abacus-gene BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \ - evolverNSbranchsites evolverNSsites pamp yn00 + evolverNSbranchsites evolverNSsites infinitesites mcmctree 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} + ${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}${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 diff --git a/biology/paml/distinfo b/biology/paml/distinfo index c6e205ca7ab2..f52a021a50de 100644 --- a/biology/paml/distinfo +++ b/biology/paml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1574435935 -SHA256 (paml4.9j.tgz) = 97aac6cb8f23844202545e9ba4e42020231c2a30051b36f4e4d2f423e270d461 -SIZE (paml4.9j.tgz) = 6562281 +TIMESTAMP = 1661485713 +SHA256 (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 1bb40ea7c976d961a4f46b76e950423f6f252d7060bc621cbf29c9743b88a063 +SIZE (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 3393889 diff --git a/biology/paml/files/patch-src_paml.h b/biology/paml/files/patch-src_paml.h deleted file mode 100644 index c7e35c89038f..000000000000 --- a/biology/paml/files/patch-src_paml.h +++ /dev/null @@ -1,14 +0,0 @@ ---- src/paml.h.orig 2020-08-20 16:14:50 UTC -+++ src/paml.h -@@ -372,9 +372,9 @@ void copySptree(void); - void printSptree(void); - - --enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; -+enum SeqTypes {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq}; - --enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; -+enum OutTreeOptions {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32}; - - - /* use mean (0; default) for discrete gamma instead of median (1) */ diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist index 9c0041d7c15f..8ba55f7dfe03 100644 --- a/biology/paml/pkg-plist +++ b/biology/paml/pkg-plist @@ -1,173 +1,187 @@ +bin/baseml +bin/basemlg +bin/chi2 +bin/codeml +bin/evolver +bin/evolverNSbranches +bin/evolverNSbranchsites +bin/evolverNSsites +bin/infinitesites +bin/mcmctree +bin/pamp +bin/yn00 %%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf -%%PORTDOCS%%%%DOCSDIR%%/README.txt +%%PORTDOCS%%%%DOCSDIR%%/README.md %%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/FigTree.tre %%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%%/YN00abglobin.result.txt %%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%%/myxo/codeml-M0.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl %%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