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.
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.
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)?
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