check_beast2_pkgs: Checks if 'bbt_run' has the 'BEAST2' packages needed to...

In richelbilderbeek/babette: Control 'BEAST2'

Checks if bbt_run has the 'BEAST2' packages needed to process its arguments. Will stop if not.

Description

For example, to use a Nested Sampling MCMC, the 'BEAST2' 'NS' package needs to be installed.

Usage

check_beast2_pkgs(mcmc, beast2_path = get_default_beast2_bin_path())

Arguments

mcmc	the MCMC options, see create_mcmc
beast2_path	name of either a 'BEAST2' binary file (usually simply beast) or a 'BEAST2' jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Minimal BEAST2 setup
  check_beast2_pkgs(mcmc = create_mcmc())

  # BEAST2 with NS package installed
  if (is_beast2_ns_pkg_installed()) {
    check_beast2_pkgs(mcmc = create_ns_mcmc())
  }

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

richelbilderbeek/babette documentation built on Oct. 10, 2023, 8:18 p.m.