On 3/19/12 5:19 PM, Peter Cock wrote:
Why do you need to do anything special at all for Galaxy here? I'd just write it as a single command line call which blocks. As far as Galaxy will know it is just a slow tool.
I suppose the tool could just poll the server, and only produce results when the process is complete. I could swear I read something somewhere in the Galaxy documentation that described two kinds of tools: one kind that finish quickly, and another that run for awhile (or a long while), and produce results when they're done. Maybe it was among the cloud-related documentation, about using the scheduler.
Thanks for the suggestion. I'll try polling.
The second question is, besides this mailing list, and the Galaxy wiki, is there are good online video or text resource that explains the Galaxy architecture and how to use it? The docs are good as far as they go, but most of what's in the<command> scripts in the tool files isn't documented.
There are quite a few Galaxy videos... not sure if there are any aimed at potential developers. Are you asking about the Cheetah template language used inside the XML for the<command> which is almost a scripting language in itself, or the actual wrapper scripts used in some tools (which can be written in Python, Perl, etc)?
Cheetah documentation is findable. I'm asking more about understanding how the inputs relate to what's available in Python in the Cheetah template in the <command> section. I guess there's not much for developers to get an overview: how inputs, parameters, outputs, the command, the template, and Python all work together. Seems the only way is trial, error, experiment, and trying to understand the existing tools.
Thanks
--Mark