On Tue, Nov 6, 2012 at 11:34 PM, Franco Caramia
<franco.cara...@petermac.org> wrote:
> Yes, primer3 is available as a command line tool, it was just an example,
> the one I'm actually after is optimus primer..
> I'm sure there are several web-tools out there that would be nice to get to
> Galaxy...
> Any Ideas??

Galaxy does have some tools which fetch data from an online resource,
for example BioMoby, UCSC, etc. Many of these call into another
website (i.e. don't have to pass any Galaxy information to the 3rd
party) so are not suitable. The "Get Microbial Data" does start with a
Galaxy tool interface allowing you to pick options...

However, I am not aware of any truly analogous examples to what
you want. In your shoes what I would do is write a 'stand alone'
command line script which Galaxy can call like any other tool (you
write an XML file specifying the inputs, e.g. a FASTA file).

Your custom script must then call the 3rd party website, set any
options, upload any input files (e.g. a FASTA file of sequences),
and then wait for the remote service to finish, download the data,
perhaps parse the HTML to reformat it into something more useful
like a tabular file - and then finish. You'd need lots of error handling
too of course ;)

The critical point here is your wrapper script will block - it will
keep running (e.g. in a sleep and poll loop) until the remote site
finishes or fails, and only then return the results to Galaxy.
i.e. From Galaxy's perspective it will be a simple command line
which just takes a while to run.

If the remote site provides a web API this might not be too hard.
If their only interface is intended for human usage, then technically
it might not be very easy. If you have to collect results via email
it will be even more complicated.

Also, check the remote site's terms and conditions, wrapping it
in Galaxy may not be permitted. Contact the site owners - they
may prefer to release their own binaries with a Galaxy wrapper?

Regards,

Peter
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