diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fcca9ef115..6ca257245a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11269,56 +11269,63 @@ (define-public mrbayes "1c4qg4wd6lhj1if5g6462pk15bhh7v84ys92sp47yih7lrkk2jd6")))) (properties `((upstream-name . "MrBayes"))) (build-system gnu-build-system) + (arguments + (list + #:configure-flags '(list "--enable-sse=no" + "--enable-avx=no" + "--enable-fma=no" + "--with-mpi" + "--without-beagle") + #:phases + `(modify-phases %standard-phases + (add-after 'unpack 'do-not-detect-CPU-features + (lambda _ + (delete-file "configure") + (delete-file "aclocal.m4") + (substitute* "configure.ac" + (("AC_CONFIG_AUX_DIR.*") "") + (("AC_CONFIG_MACRO_DIRS.*") "") + (("^AX_EXT") ""))))))) + (inputs + (list openmpi)) (native-inputs - (list automake - autoconf)) + (list autoconf autoconf-archive automake pkg-config)) (home-page "https://github.com/NBISweden/MrBayes/") (synopsis "Bayesian inference of phylogeny") (description - "@code{MrBayes} is a program for Bayesian inference and model choice across -a wide range of phylogenetic and evolutionary models. @code{MrBayes} uses @dfn{ -MCMC} (Markov chain Monte Carlo) methods to estimate the posterior distribution -of model parameters. Program features include: + "@code{MrBayes} is a program for Bayesian inference and model choice +across a wide range of phylogenetic and evolutionary models. @code{MrBayes} +uses @dfn{MCMC} (Markov chain Monte Carlo) methods to estimate the posterior +distribution of model parameters. Program features include: + @itemize -@item -analysis of nucleotide, amino acid, restriction site, and morphological data; -@item -mixing of data types, such as molecular and morphological characters, in a single -analysis; -@item -easy linking and unlinking of parameters across data partitions; -@item -multiple evolutionary models, including 4x4, doublet, and codon models for -nucleotide data and many of the standard rate matrices for amino acid data; -@item -estimation of positively selected sites in a fully hierarchical Bayesian framework; -@item -full integration of the @code{BEST} algorithms for the multi-species coalescent; -@item -estimation of time calibrated (clock) trees using a variety of (strict and) -relaxed-clock models; -@item -support for complex combinations of positive, negative, and backbone constraints -on topologies; -@item -model jumping across the @code{GTR} model space and across fixed rate matrices -for amino acid data; -@item -monitoring of convergence during the analysis, and access to a wide range of -convergence diagnostics tools after the analysis has finished; -@item -rich summaries of posterior samples of branch and node parameters printed to -majority rule consensus trees in FigTree format; -@item -implementation of the stepping-stone method for accurate estimation of model -likelihoods for Bayesian model choice using Bayes factors; -@item -ability to spread jobs over a cluster of computers using @code{MPI} (for -Macintosh and UNIX environments only); -@item -support for the @code{BEAGLE} library, resulting in dramatic speedups for codon -and amino acid models on compatible hardware (NVIDIA graphics cards); -@end itemize") +@item analysis of nucleotide, amino acid, restriction site, and morphological + data; +@item mixing of data types, such as molecular and morphological characters, in + a single analysis; +@item easy linking and unlinking of parameters across data partitions; +@item multiple evolutionary models, including 4x4, doublet, and codon models + for nucleotide data and many of the standard rate matrices for amino acid + data; +@item estimation of positively selected sites in a fully hierarchical Bayesian + framework; +@item full integration of the @code{BEST} algorithms for the multi-species + coalescent; +@item estimation of time calibrated trees using a variety of (strict and) + relaxed-clock models; +@item support for complex combinations of positive, negative, and backbone + constraints on topologies; +@item model jumping across the @code{GTR} model space and across fixed rate + matrices for amino acid data; +@item monitoring of convergence during the analysis, and access to a wide + range of convergence diagnostics tools after the analysis has finished; +@item rich summaries of posterior samples of branch and node parameters + printed to majority rule consensus trees in FigTree format; +@item implementation of the stepping-stone method for accurate estimation of + model likelihoods for Bayesian model choice using Bayes factors; +@item ability to spread jobs over a cluster of computers using @code{MPI}. +@end itemize +") (license license:gpl3))) (define-public sjcount