Usage

Using Docker (Recommended)

If you installed FAVITES using the Docker image (recommended), you can run FAVITES using run_favites_docker.py:

usage: run_favites_docker.py [-h] -c CONFIG [-o OUT_DIR] [-v] [-u [VERSION]]

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Configuration file (default: None)
  -o OUT_DIR, --out_dir OUT_DIR
                        Output directory (default: None)
  -v, --verbose         Print verbose messages to stderr (default: False)
  -u [VERSION], --update [VERSION]
                        Update Docker image (-u to pull newest version, -u <VERSION> to pull <VERSION>) (default: None)

Running run_favites_docker.py with the -u flag will pull the latest Docker image before running, and running it with -u VERSION (e.g. -u 1.0.0) will pull the Docker image for FAVITES version VERSION specifically. The Docker version should be run without sudo.

Running via Singularity

If you installed FAVITES using Singularity (recommended), you can run FAVITES using run_favites_singularity.py. Note that you must specify a version number using -u, and note that run_favites_singularity.py is only compatible with FAVITES version 1.1.7 onward.

usage: run_favites_singularity.py [-h] -c CONFIG [-o OUT_DIR] [-v] -u [VERSION]

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Configuration file (default: None)
  -o OUT_DIR, --out_dir OUT_DIR
                        Output directory (default: None)
  -v, --verbose         Print verbose messages to stderr (default: False)
  -u [VERSION], --update [VERSION]
                        Update Docker image (-u to pull newest version, -u <VERSION> to pull <VERSION>) (default: None)

Manually-Installed FAVITES

If you cloned the repository and installed the dependencies manually (i.e., you're not using the Docker image), you can run FAVITES using run_favites.py:

usage: run_favites.py [-h] -c CONFIG [-o OUT_DIR] [-s RANDOM_NUMBER_SEED] [-v]

FAVITES: FrAmework for VIral Transmission and Evolution Simulation

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Configuration file (default: None)
  -o OUT_DIR, --out_dir OUT_DIR
                        Output directory (default: None)
  -v, --verbose         Print verbose messages to stderr (default: False)

Note that, to run FAVITES, you must have a configuration file (CONFIG in the usage message) in the format we require. We have included an example configuration file as well as examples of other FAVITES files in the example folder. Refer to the File Formats section of the Wiki for more information.

Also, for some reason, you must execute the run_favites.py script (and not run it as an argument to the python3 executable). In other words, PATH_TO_FAVITES/run_favites.py should work, but python3 PATH_TO_FAVITES/run_favites.py will likely not.