On 03/19/2012 10:19 PM, Peter Cock wrote:
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.

Yes, Galaxy is pretty good with handling 'slow' tools (ie: you can close the browser, and come back next morning)

However, we have one tool where we just use Galaxy to execute a job which manipulates data outside of the Galaxy data directory. We do something similar to what you have asked for initially:

We have a perl wrapper, which first submits the job using "IPC::Open3", followed by a 'while' loop checking the status of the job and finally produces a 'log' file which ends up as the new galaxy history item.


Regards, Hans


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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