On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnson <mjohn...@ncbi.nlm.nih.gov> wrote:
> I'm writing some tools to integrate NCBI data resources with Galaxy. I have
> two questions.
>
> The first is simple. I want to write a tool for a long-running process that
> is handled by some other scheduler, and that produces its own job ids. Some
> web services, like BLAST, for example, receive a request, and take a while
> to complete processing. The job id can be used to fetch either job status or
> results from the server, depending on whether it has completed. How do you
> make a Galaxy tool that polls the server, and produces an output set only
> when the process is complete?

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.

> 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)?

Peter
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