hyphy Module

Define a custom HyPhy build/install.

class hyphy.HyPhy(**kwargs)

Bases: object

This class creates a HyPhy instance. Generally this is only necessary to use if any of these applies:
  • You wish to use a local build of HyPhy (not a canonically installed build)
  • You wish to use a local install of HyPhy (installed elsewhere from /usr/local)
  • You wish to use a different HyPhy executable from the default, which is HYPHYMP

Initiliaze a HyPhy() instance.

Optional keyword arguments:
  1. executable, the desired executable to use (ie HYPHYMPI). Default: HYPHYMP.
  2. build_path, the path to a local hyphy build. Use this argument if you have compiled hyphy in the downloaded hyphy/ directory and did not run make install
  3. install_path, the path to a hyphy install. Use this argument if you have specified a different installation path for hyphy, i.e. you provided -DINSTALL_PREFIX=/other/path/ to cmake.
  4. cpu, the maximum number of processes per analysis. By default, HyPhy will take as many CPUs as it can/requires. This argument will limit the maximum. Default: None
  5. quiet, suppress screen output (Note, HyPhy will still creates messages.log and errors.log files, when applicable). Default: False
  6. suppress_log, suppress messages.log and errors.log files. Default: False.
  7. mpi_launcher, mpi launcher. Default: mpirun. Use this argument if are you specifying HYPHYMPI for executable.
  8. mpi_options, options to pass to the mpi launcher. Default: “”.

Examples:

>>> ### Define a HyPhy() object, specifying a quiet analysis (no console output) with no log files output
>>> my_hyphy = HyPhy(quiet = True, suppress_log = True)

>>> ### Define a HyPhy() object, specifying that a maximum of 4 processes be used (for the default executable HYPHYMP)
>>> my_hyphy = HyPhy(CPU = 4)

>>> ### Define a HyPhy() object, specifying a specific *build path*
>>> my_hyphy = HyPhy(build_path = "/path/to/local/build/hyphy/")

>>> ### Define a HyPhy() object, specifying a specific *install path*
>>> my_hyphy = HyPhy(install_path = "/path/to/local/install/hyphy/")               

>>> ### Define a HyPhy() object, specifying that HYPHYMPI be used, with associated arguments for mpirun to use 32 processes
>>> my_hyphy = HyPhy(executable = "HYPHYMPI", mpi_launcher = "mpirun", mpi_options = "-np 32")