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)?

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to