I am investigating into if I can use a library like GHMM with my python web service in which runs on AppEngine.
Short answer: no
https://developers.google.com/appengine/kb/commontasks
What third party libraries can I use in my application?
You can use any pure Python third party libraries in your Google App Engine application. In order to use a third party library, simply include the files in your application's directory, and they will be uploaded with your application when you deploy it to our system. You can import the files as you would any other Python files with your application.
As @gahooa has said, the generic answer is no.
For more popular libraries that have C dependencies your best option right now is to file a ticket[1], get other to upvote (star) your ticket and have the App Engine add it as a supported library.
[1] http://code.google.com/p/googleappengine/issues/entry?template=Feature%20request
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