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Usage via iMicrobe
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PuMA is also available through `iMicrobe <https://www.imicrobe.us>`_.
You will need to create a `Cyverse Account <https://user.cyverse.org/login?redirect=%7B%22pathname%22%3A%22%2Fservices%2Fmine%22%2C%22query%22%3A%7B%7D%7D>`_. Once you do this, head to the `iMicrobe website <https://www.imicrobe.us>`_ and click on 'My Account'-> 'Data Store'. Once you are in the Data Store, you will be able to upload the input files to use for PuMA. 


 
Once you have uploaded the input files in the Data Store, nagivate to 'Tools' -> 'Apps' and click on 'puma-x.x.xux' (most current version). You will then be able to select the input file or copy and paste the contents of the file into the appropriate box. 



iMicrobe accesses the `Extreme Science and Engineering Discovery Environment <https://www.xsede.org>`_ (XSEDE) compute resources at Texas Advanced Computing Center (TACC) including Stampede2. **While this offers access to significant compute power, due the large number of users the job might be in the queue for hours.** Once the job runs, it takes a few seconds for execution to complete. 



To learn more about iMicrobe and Stampede2:

- `iMicrobe Documentation <https://hurwitzlab.gitbook.io/imicrobe/>`_ 

- `Stampede2 Documentation <https://www.tacc.utexas.edu/systems/stampede2>`_