Excerpts from Sonali Amonkar's message of Sun Jan 16 17:17:14 +0000 2011:
I agree what you mentioned on Tools. Does Galaxy have any provision for executing Workflows from command line too?
Currently I don't think this is implemented, but the plan is that this would be done through the API.
At initial glance I was unable to figure out what the scripts are for(am basically not familiar with Python). Until I try to figure that out, can you just let me know whether, in the first place, if Galaxy does provide (or has a Beta version planned of) some API library (say Galaxy.tar) which I can pick up and put in my Java project and then create workflows & tools?
Galaxy is primarily a web application, and the API provided is REST / HTTP based. The python scripts are command line wrappers for accessing this. If you want to use the API from a Java application, you would just access it directly through the web. We do not provide any special support for Java, but you are welcome to contribute and API wrapper.
Thanks, James