Local Usage (MacOS or Linux)

Follow the directions below to run PuMA locally without using Docker. If you want to execute PuMA with Docker, refer to the “Usage via Docker” page.

Due to dependencies, PuMA only runs on MacOS or Linux operating systems. Refer to the ‘Dependency Information’ section for more information.

After the dependencies have been installed, from Github download the ‘data_dir’ folder and within the ‘scripts’ directory download ‘run_puma.py’ and ‘puma.py’.

To execute PuMA, make sure ‘run_puma.py’ is excecutable:

chmod +x run_puma.py

Minimum PuMA execuation command:

./run_puma.py -i HPV16REF.fa -D warning

All files and folders need to be in the same location or absolute path needs to be used. For example the input file above (HPV16REF) and the ‘data_dir’ folder need to be in the same folder as ‘run_puma.py’ and ‘puma.py’.

You can always use ‘-h’ or ‘–help’ on ‘run_puma.py’ to get a list and description of all inputs.

After execution, it is encouraged to either move, rename, or delete the output folder ‘puma_out’ before running PuMA again. This way, there are no issues with the existing ‘puma_out’ folder and the new one that will be generated with each execution.